PDB-2nvh: Determination of Solvent Content in Cavities in Interleukin-1 Usi...

ID or keywords:

Entry

Database: PDB / ID: 2nvh

Title

Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density

Components

Interleukin-1 beta

Keywords

CYTOKINE / Water / Hydration / Protein folding

Function / homology

Function and homology information

smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / : / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of lipid catabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of glial cell proliferation / JNK cascade / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / embryo implantation / response to interleukin-1 / positive regulation of mitotic nuclear division / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / negative regulation of MAP kinase activity / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / Interleukin-1 signaling / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / immune response / protein domain specific binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

MAD / Resolution: 1.53 Å

Authors

Quillin, M.L. / Matthews, B.W.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Determination of solvent content in cavities in IL-1beta using experimentally phased electron density
Authors: Quillin, M.L. / Wingfield, P.T. / Matthews, B.W.

History

Deposition	Nov 12, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nvh.cif.gz	50.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2nvh.ent.gz	32.4 KB	Display	PDB format
PDBx/mmJSON format	2nvh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nvh_validation.pdf.gz	435.4 KB	Display	wwPDB validaton report
Full document	2nvh_full_validation.pdf.gz	443 KB	Display
Data in XML	2nvh_validation.xml.gz	10.8 KB	Display
Data in CIF	2nvh_validation.cif.gz	14.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nv/2nvh ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nvh	HTTPS FTP

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Related structure data

Related structure data	5i1bS S: Starting model for refinement
Similar structure data	1s0l-d 1twm-d 5r8h-d 1ino-d 5r8i-d 1tp0-d 4lxd-d 5r8c-d 1t4q-d 1i1b-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#214 - Oct 2017 Chimeric Antigen Receptors similarity (13) #122 - Feb 2010 Enhanceosome similarity (4) #56 - Aug 2004 Caspases similarity (3) #224 - Aug 2018 Legumain similarity (3) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#214 - Oct 2017
Chimeric Antigen Receptors
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#79 - Jul 2006
Amyloid-beta Precursor Protein
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Vascular Endothelial Growth Factor (VegF
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#213 - Sep 2017
Sirtuins
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Deposited unit

A: Interleukin-1 beta

hetero molecules

17.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	54.506, 54.506, 75.359
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Interleukin-1 beta / IL-1 beta / Catabolin Mass: 17395.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.75 %
Crystal grow	Temperature: 298 K / pH: 7.5 Details: Well solution of 2.2 - 2.8 M ammonium sulfate, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
4		1

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 1999

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

D res low: 60 Å

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
1	13.3	319609	0.04	1.05	1.5	35259	99.9
2	7.4	90028	0.056	0.83	2.1	12740	99.5
3	7.1	87402	0.066	0.96	2.1	12749	99.6
4	7.3	89041	0.061	0.88	2.1	12749	99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
3.23	60	99.4	1	0.032	1.129
2.56	3.23	99.9	1	0.033	1.231
2.24	2.56	100	1	0.037	1.284
2.04	2.24	100	1	0.041	1.255
1.89	2.04	100	1	0.054	1.146
1.78	1.89	100	1	0.077	1.042
1.69	1.78	100	1	0.112	0.956
1.62	1.69	100	1	0.166	0.862
1.55	1.62	100	1	0.217	0.831
1.5	1.55	100	1	0.298	0.776
4.52	60	97.2	2	0.053	0.834
3.59	4.52	99	2	0.042	0.763
3.14	3.59	99.7	2	0.047	0.909
2.85	3.14	100	2	0.058	0.927
2.65	2.85	99.7	2	0.077	0.881
2.49	2.65	99.7	2	0.101	0.857
2.37	2.49	100	2	0.129	0.824
2.26	2.37	100	2	0.169	0.784
2.18	2.26	100	2	0.216	0.775
2.1	2.18	100	2	0.298	0.743
4.52	60	97.4	3	0.062	1
3.59	4.52	99.5	3	0.053	1.009
3.14	3.59	99.7	3	0.057	1.111
2.85	3.14	100	3	0.069	1.165
2.65	2.85	99.7	3	0.09	1.069
2.49	2.65	99.7	3	0.115	0.995
2.37	2.49	100	3	0.152	0.926
2.26	2.37	100	3	0.19	0.834
2.18	2.26	100	3	0.242	0.792
2.1	2.18	100	3	0.333	0.753
4.52	60	97.4	4	0.058	0.91
3.59	4.52	99.4	4	0.047	0.871
3.14	3.59	99.8	4	0.051	0.988
2.85	3.14	100	4	0.062	0.993
2.65	2.85	99.7	4	0.084	0.991
2.49	2.65	99.8	4	0.105	0.938
2.37	2.49	100	4	0.138	0.861
2.26	2.37	99.9	4	0.183	0.788
2.18	2.26	100	4	0.226	0.771
2.1	2.18	100	4	0.309	0.733

Reflection

Resolution: 1.5→27.2 Å / Num. obs: 35259 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / B_iso Wilson estimate: 19.5 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 64

Reflection shell

Resolution: 1.5→1.55 Å / R_merge(I) obs: 0.298 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 38.54 Å / FOM acentric: 0.835 / FOM centric: 0.9 / Reflection acentric: 12223 / Reflection centric: 427

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.1	38.54	0	0	12221	426
ISO_2	2.1	38.54	5.001	2.172	11975	416
ISO_3	2.1	38.54	4.842	2.234	11688	416
ISO_4	2.1	38.54	5.106	2.301	11867	417
ANO_1	2.1	38.54	0	0	0	0
ANO_2	2.1	38.54	1.223	0	11909	0
ANO_3	2.1	38.54	1.335	0	11483	0
ANO_4	2.1	38.54	1.295	0	11749	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	9.14-38.54	0	0	121	22
ISO_1	6.55-9.14	0	0	245	25
ISO_1	5.38-6.55	0	0	321	24
ISO_1	4.67-5.38	0	0	378	25
ISO_1	4.18-4.67	0	0	417	20
ISO_1	3.82-4.18	0	0	480	25
ISO_1	3.54-3.82	0	0	529	22
ISO_1	3.31-3.54	0	0	564	23
ISO_1	3.12-3.31	0	0	596	19
ISO_1	2.97-3.12	0	0	630	21
ISO_1	2.83-2.97	0	0	674	24
ISO_1	2.71-2.83	0	0	698	19
ISO_1	2.6-2.71	0	0	734	19
ISO_1	2.51-2.6	0	0	761	23
ISO_1	2.42-2.51	0	0	788	20
ISO_1	2.35-2.42	0	0	817	19
ISO_1	2.28-2.35	0	0	822	17
ISO_1	2.21-2.28	0	0	862	22
ISO_1	2.15-2.21	0	0	889	21
ISO_1	2.1-2.15	0	0	895	16
ANO_1	9.14-38.54	0	0	0	0
ANO_1	6.55-9.14	0	0	0	0
ANO_1	5.38-6.55	0	0	0	0
ANO_1	4.67-5.38	0	0	0	0
ANO_1	4.18-4.67	0	0	0	0
ANO_1	3.82-4.18	0	0	0	0
ANO_1	3.54-3.82	0	0	0	0
ANO_1	3.31-3.54	0	0	0	0
ANO_1	3.12-3.31	0	0	0	0
ANO_1	2.97-3.12	0	0	0	0
ANO_1	2.83-2.97	0	0	0	0
ANO_1	2.71-2.83	0	0	0	0
ANO_1	2.6-2.71	0	0	0	0
ANO_1	2.51-2.6	0	0	0	0
ANO_1	2.42-2.51	0	0	0	0
ANO_1	2.35-2.42	0	0	0	0
ANO_1	2.28-2.35	0	0	0	0
ANO_1	2.21-2.28	0	0	0	0
ANO_1	2.15-2.21	0	0	0	0
ANO_1	2.1-2.15	0	0	0	0
ISO_2	9.14-38.54	10.353	3.865	107	20
ISO_2	6.55-9.14	7.242	2.488	231	25
ISO_2	5.38-6.55	8.864	2.264	299	24
ISO_2	4.67-5.38	6.943	1.346	361	25
ISO_2	4.18-4.67	4.574	1.859	409	19
ISO_2	3.82-4.18	4.402	1.603	466	23
ISO_2	3.54-3.82	3.718	1.835	524	22
ISO_2	3.31-3.54	3.834	1.372	560	22
ISO_2	3.12-3.31	3.769	1.283	594	19
ISO_2	2.97-3.12	3.936	1.962	626	21
ISO_2	2.83-2.97	3.896	1.457	673	23
ISO_2	2.71-2.83	4.174	2.09	695	19
ISO_2	2.6-2.71	4.443	1.662	734	19
ISO_2	2.51-2.6	4.213	1.898	759	22
ISO_2	2.42-2.51	4.181	2.278	788	20
ISO_2	2.35-2.42	4.005	1.639	817	19
ISO_2	2.28-2.35	3.793	1.361	822	17
ISO_2	2.21-2.28	3.454	1.854	862	22
ISO_2	2.15-2.21	3.415	1.591	889	21
ISO_2	2.1-2.15	3.108	1.374	759	14
ANO_2	9.14-38.54	1.194	0	98	0
ANO_2	6.55-9.14	1.439	0	216	0
ANO_2	5.38-6.55	1.607	0	287	0
ANO_2	4.67-5.38	1.503	0	353	0
ANO_2	4.18-4.67	1.409	0	408	0
ANO_2	3.82-4.18	1.59	0	461	0
ANO_2	3.54-3.82	1.457	0	520	0
ANO_2	3.31-3.54	1.593	0	554	0
ANO_2	3.12-3.31	1.539	0	594	0
ANO_2	2.97-3.12	1.498	0	623	0
ANO_2	2.83-2.97	1.375	0	672	0
ANO_2	2.71-2.83	1.247	0	695	0
ANO_2	2.6-2.71	1.081	0	735	0
ANO_2	2.51-2.6	0.95	0	759	0
ANO_2	2.42-2.51	0.776	0	788	0
ANO_2	2.35-2.42	0.734	0	817	0
ANO_2	2.28-2.35	0.567	0	821	0
ANO_2	2.21-2.28	0.489	0	862	0
ANO_2	2.15-2.21	0.44	0	887	0
ANO_2	2.1-2.15	0.368	0	759	0
ISO_3	9.14-38.54	10.087	4.275	97	20
ISO_3	6.55-9.14	6.908	2.587	213	25
ISO_3	5.38-6.55	8.227	2.285	273	24
ISO_3	4.67-5.38	6.756	1.375	336	25
ISO_3	4.18-4.67	4.467	1.886	383	19
ISO_3	3.82-4.18	4.39	1.624	444	23
ISO_3	3.54-3.82	3.731	1.823	490	22
ISO_3	3.31-3.54	3.792	1.388	512	22
ISO_3	3.12-3.31	3.748	1.316	565	19
ISO_3	2.97-3.12	3.924	2.016	603	21
ISO_3	2.83-2.97	3.94	1.502	662	23
ISO_3	2.71-2.83	4.247	2.154	690	19
ISO_3	2.6-2.71	4.496	1.703	729	19
ISO_3	2.51-2.6	4.301	1.982	754	22
ISO_3	2.42-2.51	4.22	2.476	788	20
ISO_3	2.35-2.42	4.103	1.53	817	19
ISO_3	2.28-2.35	3.891	1.426	822	17
ISO_3	2.21-2.28	3.509	2.097	862	22
ISO_3	2.15-2.21	3.566	1.846	889	21
ISO_3	2.1-2.15	3.2	1.411	759	14
ANO_3	9.14-38.54	1.415	0	76	0
ANO_3	6.55-9.14	1.545	0	190	0
ANO_3	5.38-6.55	1.511	0	239	0
ANO_3	4.67-5.38	1.524	0	305	0
ANO_3	4.18-4.67	1.386	0	372	0
ANO_3	3.82-4.18	1.539	0	420	0
ANO_3	3.54-3.82	1.499	0	476	0
ANO_3	3.31-3.54	1.67	0	496	0
ANO_3	3.12-3.31	1.648	0	554	0
ANO_3	2.97-3.12	1.68	0	596	0
ANO_3	2.83-2.97	1.562	0	656	0
ANO_3	2.71-2.83	1.402	0	684	0
ANO_3	2.6-2.71	1.269	0	728	0
ANO_3	2.51-2.6	1.124	0	754	0
ANO_3	2.42-2.51	0.936	0	788	0
ANO_3	2.35-2.42	0.899	0	817	0
ANO_3	2.28-2.35	0.745	0	822	0
ANO_3	2.21-2.28	0.64	0	862	0
ANO_3	2.15-2.21	0.586	0	889	0
ANO_3	2.1-2.15	0.518	0	759	0
ISO_4	9.14-38.54	9.828	4.1	101	20
ISO_4	6.55-9.14	7.419	2.745	219	25
ISO_4	5.38-6.55	8.622	2.48	280	24
ISO_4	4.67-5.38	6.854	1.401	349	25
ISO_4	4.18-4.67	4.598	1.724	396	20
ISO_4	3.82-4.18	4.663	1.736	461	23
ISO_4	3.54-3.82	4.026	1.965	521	22
ISO_4	3.31-3.54	4.03	1.438	542	22
ISO_4	3.12-3.31	3.977	1.383	589	19
ISO_4	2.97-3.12	4.128	2.051	619	21
ISO_4	2.83-2.97	4.161	1.533	668	23
ISO_4	2.71-2.83	4.403	2.415	695	19
ISO_4	2.6-2.71	4.624	1.704	734	19
ISO_4	2.51-2.6	4.447	1.995	756	22
ISO_4	2.42-2.51	4.416	2.44	788	20
ISO_4	2.35-2.42	4.211	1.611	817	19
ISO_4	2.28-2.35	4.002	1.571	822	17
ISO_4	2.21-2.28	3.607	2.011	862	22
ISO_4	2.15-2.21	3.556	2.077	889	21
ISO_4	2.1-2.15	3.264	1.516	759	14
ANO_4	9.14-38.54	1.11	0	88	0
ANO_4	6.55-9.14	1.567	0	207	0
ANO_4	5.38-6.55	1.602	0	265	0
ANO_4	4.67-5.38	1.463	0	329	0
ANO_4	4.18-4.67	1.462	0	393	0
ANO_4	3.82-4.18	1.662	0	447	0
ANO_4	3.54-3.82	1.558	0	503	0
ANO_4	3.31-3.54	1.709	0	531	0
ANO_4	3.12-3.31	1.608	0	583	0
ANO_4	2.97-3.12	1.591	0	616	0
ANO_4	2.83-2.97	1.507	0	666	0
ANO_4	2.71-2.83	1.283	0	694	0
ANO_4	2.6-2.71	1.256	0	735	0
ANO_4	2.51-2.6	1.024	0	756	0
ANO_4	2.42-2.51	0.842	0	788	0
ANO_4	2.35-2.42	0.786	0	817	0
ANO_4	2.28-2.35	0.684	0	822	0
ANO_4	2.21-2.28	0.592	0	861	0
ANO_4	2.15-2.21	0.501	0	889	0
ANO_4	2.1-2.15	0.464	0	759	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	Occupancy
1	1.59	7.77	3.244	PT	1.24
2	25.601	15.986	2.601	PT	0.59
3	47.331	4.228	4.46	PT	0.72
4	24.229	13.066	3.957	PT	0.58
5	43.622	3.914	2.939	PT	0.33
6	16.106	51.609	5.376	PT	0.78
7	3.05	8.298	2.755	PT	0.65

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
9.14-38.54	0.934	0.899	122	23
6.55-9.14	0.944	0.982	245	25
5.38-6.55	0.919	0.991	321	24
4.67-5.38	0.933	0.99	378	25
4.18-4.67	0.921	0.862	417	20
3.82-4.18	0.928	0.875	480	25
3.54-3.82	0.917	0.895	529	22
3.31-3.54	0.936	0.748	564	23
3.12-3.31	0.913	0.883	596	19
2.97-3.12	0.925	0.974	630	21
2.83-2.97	0.906	0.884	674	24
2.71-2.83	0.898	0.944	698	19
2.6-2.71	0.884	0.943	735	19
2.51-2.6	0.85	0.928	761	23
2.42-2.51	0.837	0.879	788	20
2.35-2.42	0.804	0.942	817	19
2.28-2.35	0.764	0.84	822	17
2.21-2.28	0.723	0.885	862	22
2.15-2.21	0.709	0.806	889	21
2.1-2.15	0.578	0.799	895	16

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
TNT		refinement
PDB_EXTRACT	2	data extraction
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5I1B

5i1b

Resolution: 1.53→27.2 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT

	R_factor	Num. reflection	% reflection
all	0.211	35287	-
obs	0.211	35225	100 %

Solvent computation

Solvent model: MOEWS AND KRETSINGER / B_sol: 233.11 Å² / k_sol: 0.87 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.53→27.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1224	0	10	149	1383

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Weight
X-RAY DIFFRACTION	t_bond_d	0.025	1255	0.8
X-RAY DIFFRACTION	t_angle_deg	2.946	1681	1.3
X-RAY DIFFRACTION	t_dihedral_angle_d	18.684	760	0
X-RAY DIFFRACTION	t_incorr_chiral_ct		0
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes	0.012	40	2
X-RAY DIFFRACTION	t_gen_planes	0.021	170	5
X-RAY DIFFRACTION	t_it	14.285	1247	0
X-RAY DIFFRACTION	t_nbd	0.039	35	10

LS refinement shell

Resolution (Å)	R_factor R_work	Refine-ID	R_factor all	Total num. of bins used
1.53-1.58	0.33	X-RAY DIFFRACTION	0.36	10
1.58-1.65	0.3	X-RAY DIFFRACTION	0.33	10
1.65-1.73	0.29	X-RAY DIFFRACTION	0.32	10
1.73-1.83	0.26	X-RAY DIFFRACTION	0.29	10
1.83-1.96	0.25	X-RAY DIFFRACTION	0.28	10
1.96-2.13	0.23	X-RAY DIFFRACTION	0.25	10
2.13-2.38	0.21	X-RAY DIFFRACTION	0.23	10
2.38-2.82	0.2	X-RAY DIFFRACTION	0.22	10
2.82-4.07	0.18	X-RAY DIFFRACTION	0.2	10
4.07-27.217	0.19	X-RAY DIFFRACTION	0.24	10

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