PDB-4htn: Mitigation of X-ray damage in macromolecular crystallography by s...

ID or keywords:

Entry

Database: PDB / ID: 4htn

Title

Mitigation of X-ray damage in macromolecular crystallography by submicrometer line focusing; total dose 1.32 x 10e+12 X-ray photons

Components

Lysozyme C

Keywords

HYDROLASE / O-GLYCOSYL / GLYCOSIDASE

Function / homology

Function and homology information

Antimicrobial peptides / Neutrophil degranulation /

beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process /

lysozyme /

lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.3 Å

Authors

Duke, N.E.C. / Finfrock, Y.Z. / Stern, E.A. / Alkire, R.W. / Lazarski, K. / Joachimiak, A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing.
Authors: Finfrock, Y.Z. / Stern, E.A. / Alkire, R.W. / Kas, J.J. / Evans-Lutterodt, K. / Stein, A. / Duke, N. / Lazarski, K. / Joachimiak, A.

History

Deposition	Nov 1, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Sep 20, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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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PDBx/mmCIF format	4htn.cif.gz	78.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4htn.ent.gz	55.9 KB	Display	PDB format
PDBx/mmJSON format	4htn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/4htn ftp://data.pdbj.org/pub/pdb/validation_reports/ht/4htn	HTTPS FTP

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Related structure data

Related structure data	4htkC 4htqC 1lz8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hll-d 3agg-d 1lsa-d 6yob-d 2f4a-d 5la5-d 7cdq-d 6q8r-d 2x0a-d 2h9j-d 7bvo-d 5o6q-d 1gbz-d 4hv1-d 5b06-d 3lzt-d 6agn-d 4h93-d 5k2n-d 4wld-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	#21 - Sep 2001 Antibodies similarity (2) #136 - Apr 2011 Nanobodies similarity (2) #222 - Jun 2018 Proteins and Nanoparticles similarity (2) #9 - Sep 2000 Lysozyme similarity (2) #142 - Oct 2011 PDB Pioneers similarity (2)

Deposited unit

A: Lysozyme C

hetero molecules

14.8 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)	78.958, 78.958, 36.881
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-323- HOH
2	1	A-428- HOH

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.01 Å³/Da / Density % sol: 38.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.73 Details: 0.100M sodium acetate, pH 4.73, 5% sodium chloride (w/v), 25% ethylene glycol (v/v), micro-seeded, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.66658 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2012

Radiation

Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.66658 Å / Relative weight: 1

Reflection

Redundancy: 7.2 % / Av σ(I) over netI: 30.86 / Number: 207833 / R_merge(I) obs: 0.064 / Χ²: 0.95 / D res high: 1.3 Å / D res low: 100 Å / Num. obs: 29053 / % possible obs: 99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.45	100	98.4	1	0.022	0.705	6.2
3.53	4.45	100	1	0.021	0.77	6.9
3.08	3.53	100	1	0.023	0.821	7.1
2.8	3.08	99.5	1	0.028	0.884	7
2.6	2.8	99.9	1	0.034	0.948	6.8
2.45	2.6	99.7	1	0.037	0.967	7
2.32	2.45	100	1	0.041	1.018	6.6
2.22	2.32	99.6	1	0.046	1.138	6.8
2.14	2.22	99.6	1	0.053	1.202	7
2.06	2.14	100	1	0.057	1.255	7
2	2.06	99.3	1	0.065	1.253	7.1
1.94	2	100	1	0.074	1.254	7.1
1.89	1.94	99.2	1	0.08	1.246	7.1
1.84	1.89	100	1	0.094	1.262	7.2
1.8	1.84	98.9	1	0.106	1.157	7
1.76	1.8	100	1	0.111	1.112	7.2
1.73	1.76	98.5	1	0.124	1.026	7.2
1.7	1.73	100	1	0.127	1.023	7.2
1.67	1.7	98.2	1	0.143	1.006	7.3
1.64	1.67	100	1	0.149	0.991	7.2
1.61	1.64	100	1	0.153	0.968	7.3
1.59	1.61	97.7	1	0.169	0.931	7.3
1.56	1.59	100	1	0.188	0.912	7.2
1.54	1.56	100	1	0.186	0.897	7.3
1.52	1.54	97.1	1	0.23	0.918	7.3
1.5	1.52	100	1	0.221	0.903	7.2
1.48	1.5	100	1	0.243	0.912	7.3
1.46	1.48	96.9	1	0.256	0.862	7.4
1.45	1.46	99.6	1	0.272	0.844	7.2
1.43	1.45	100	1	0.288	0.86	7.3
1.42	1.43	98.9	1	0.328	0.851	7.4
1.4	1.42	96.6	1	0.351	0.872	7.4
1.39	1.4	100	1	0.355	0.818	7.3
1.37	1.39	100	1	0.362	0.786	7.4
1.36	1.37	97.6	1	0.395	0.779	7.4
1.35	1.36	97.2	1	0.429	0.806	7.3
1.33	1.35	100	1	0.465	0.81	7.2
1.32	1.33	100	1	0.461	0.8	7.4
1.31	1.32	97.7	1	0.508	0.799	7.3
1.3	1.31	96.2	1	0.502	0.795	7.4

Reflection

Resolution: 1.3→100 Å / Num. obs: 29053 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / R_merge(I) obs: 0.064 / Χ²: 0.953 / Net I/σ(I): 8.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.3-1.31	7.4	0.502	687	0.795	1	96.2
1.31-1.32	7.3	0.508	709	0.799	1	97.7
1.32-1.33	7.4	0.461	704	0.8	1	100
1.33-1.35	7.2	0.465	725	0.81	1	100
1.35-1.36	7.3	0.429	695	0.806	1	97.2
1.36-1.37	7.4	0.395	698	0.779	1	97.6
1.37-1.39	7.4	0.362	734	0.786	1	100
1.39-1.4	7.3	0.355	715	0.818	1	100
1.4-1.42	7.4	0.351	682	0.872	1	96.6
1.42-1.43	7.4	0.328	718	0.851	1	98.9
1.43-1.45	7.3	0.288	707	0.86	1	100
1.45-1.46	7.2	0.272	718	0.844	1	99.6
1.46-1.48	7.4	0.256	712	0.862	1	96.9
1.48-1.5	7.3	0.243	706	0.912	1	100
1.5-1.52	7.2	0.221	735	0.903	1	100
1.52-1.54	7.3	0.23	702	0.918	1	97.1
1.54-1.56	7.3	0.186	712	0.897	1	100
1.56-1.59	7.2	0.188	730	0.912	1	100
1.59-1.61	7.3	0.169	715	0.931	1	97.7
1.61-1.64	7.3	0.153	719	0.968	1	100
1.64-1.67	7.2	0.149	717	0.991	1	100
1.67-1.7	7.3	0.143	716	1.006	1	98.2
1.7-1.73	7.2	0.127	715	1.023	1	100
1.73-1.76	7.2	0.124	734	1.026	1	98.5
1.76-1.8	7.2	0.111	725	1.112	1	100
1.8-1.84	7	0.106	716	1.157	1	98.9
1.84-1.89	7.2	0.094	732	1.262	1	100
1.89-1.94	7.1	0.08	737	1.246	1	99.2
1.94-2	7.1	0.074	722	1.254	1	100
2-2.06	7.1	0.065	732	1.253	1	99.3
2.06-2.14	7	0.057	732	1.255	1	100
2.14-2.22	7	0.053	729	1.202	1	99.6
2.22-2.32	6.8	0.046	745	1.138	1	99.6
2.32-2.45	6.6	0.041	744	1.018	1	100
2.45-2.6	7	0.037	738	0.967	1	99.7
2.6-2.8	6.8	0.034	757	0.948	1	99.9
2.8-3.08	7	0.028	752	0.884	1	99.5
3.08-3.53	7.1	0.023	759	0.821	1	100
3.53-4.45	6.9	0.021	782	0.77	1	100
4.45-100	6.2	0.022	846	0.705	1	98.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LZ8

1lz8

Resolution: 1.3→27.916 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9338 / SU ML: 0.21 / σ(F): 1.35 / Phase error: 12.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.158	1474	5.08 %
R_work	0.1271	27543	-
obs	0.1286	29017	99.21 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.172 Å² / k_sol: 0.348 e/Å³

Displacement parameters

B_iso max: 38.66 Å² / B_iso mean: 12.5378 Å² / B_iso min: 4.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3983 Å²	0 Å²	-0 Å²
2-	-	0.3983 Å²	0 Å²
3-	-	-	-0.7967 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→27.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	21	175	1197

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	1128
X-RAY DIFFRACTION	f_angle_d	1.518	1529
X-RAY DIFFRACTION	f_chiral_restr	0.102	159
X-RAY DIFFRACTION	f_plane_restr	0.008	201
X-RAY DIFFRACTION	f_dihedral_angle_d	11.96	434

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.3002-1.3421	0.2249	124	0.1615	2432	2556	98
1.3421-1.3901	0.1757	138	0.134	2422	2560	99
1.3901-1.4458	0.1549	131	0.1169	2453	2584	99
1.4458-1.5116	0.1391	122	0.1037	2474	2596	99
1.5116-1.5912	0.1547	133	0.1002	2488	2621	99
1.5912-1.6909	0.1252	159	0.099	2438	2597	99
1.6909-1.8215	0.1557	139	0.1092	2500	2639	100
1.8215-2.0047	0.1371	140	0.1125	2489	2629	100
2.0047-2.2947	0.1628	142	0.1144	2535	2677	100
2.2947-2.8906	0.1484	125	0.1342	2578	2703	100
2.8906-27.9223	0.1751	121	0.1511	2734	2855	100

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