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- PDB-4a5g: Raphanus sativus anionic peroxidase. -

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Basic information

Entry
Database: PDB / ID: 4a5g
TitleRaphanus sativus anionic peroxidase.
ComponentsANIONIC PEROXIDASE
KeywordsOXIDOREDUCTASE / GLYCOPROTEIN
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesRAPHANUS SATIVUS (radish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJimenez-Arroyo, N. / Valderrama, B. / Gil-Rodriguez, P. / Rojas-Trejo, S.P. / Rudino-Pinera, E.
CitationJournal: To be Published
Title: Crystallographic Structure of the Raphanus Sativus Anionic Peroxidase
Authors: Gil-Rodriguez, P. / Jimenez-Arroyo, N. / Rojas-Trejo, S.P. / Rudino-Pinera, E. / Valderrama, B.
History
DepositionOct 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANIONIC PEROXIDASE
B: ANIONIC PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,73630
Polymers63,9312
Non-polymers11,80528
Water12,611700
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A: ANIONIC PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03613
Polymers31,9651
Non-polymers6,07112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANIONIC PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,70017
Polymers31,9651
Non-polymers5,73516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.148, 41.192, 137.796
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ANIONIC PEROXIDASE


Mass: 31965.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) RAPHANUS SATIVUS (radish) / Tissue: ROOT / References: UniProt: K7N5L9*PLUS, peroxidase

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Sugars , 9 types, 14 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpb1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1a_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpb1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5][a212h-1b_1-5]/1-2-1-3-4-3/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#12: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 714 molecules

#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#13: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#14: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsPOLYETHYLENE GLYCOL 6000 FRAGMENT (PG0 AND 1PE): THESE COORDINATES CORRESPOND TO VISIBLE FRAGMENTS ...POLYETHYLENE GLYCOL 6000 FRAGMENT (PG0 AND 1PE): THESE COORDINATES CORRESPOND TO VISIBLE FRAGMENTS OF PEG 6000 DETECTED IN THE ELECTRON DENSITY. SOME ATOM NAMES DERIVE FROM PEG 400 (1PE) DEFINITION.
Sequence detailsTHE SEQUENCE OF RAPHANUS SATIVUS ANIONIC PEROXIDASE HAS NEVER BEEN RELEASED. HOWEVER THE SEQUENCE ...THE SEQUENCE OF RAPHANUS SATIVUS ANIONIC PEROXIDASE HAS NEVER BEEN RELEASED. HOWEVER THE SEQUENCE REPORTED HERE SHARE AN IDENTITY OF 87.8 PER CENT WITH THE SEQUENCE DEPOSITED IN THE UNIPROT CODE Q53YQ4, ARABIDOPSIS THALIANA PEROXIDASE ATPA2. PART OF THE SEQUENCE WAS OBTAINED BY TWO MASS SPECTROMETRY SEQUENCING EXPERIMENTS, MOST OF THE PROTEIN SEQUENCE WAS EXTRACTED AND CONFIRMED FROM THE FINAL ELECTRON DENSITY MAP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 %
Description: PART OF THE PHASES WERE OBTAINED FROM THE ANOMALOUS SIGNAL COMING FROM THE IRON ATOMS AT THE HEME GROUP
Crystal growpH: 6.5
Details: THE PROTEIN CONCENTRATION WAS 50 MG/ML. THE PRECIPITANT SOLUTION COMPRISES 20% PEG 6000, 20% PEG 200, 100 MM MES PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.7329
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2010
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7329 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 51917 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 27.82 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.53 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PA2

1pa2


Resolution: 2.05→35.287 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 2116 5.1 %
Rwork0.1629 --
obs0.164 41779 99.49 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 734 700 5904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0335396
X-RAY DIFFRACTIONf_angle_d1.7277289
X-RAY DIFFRACTIONf_dihedral_angle_d15.6041692
X-RAY DIFFRACTIONf_chiral_restr0.166927
X-RAY DIFFRACTIONf_plane_restr0.011881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.09770.28141300.25122556X-RAY DIFFRACTION99
2.0977-2.15010.22841450.20892647X-RAY DIFFRACTION100
2.1501-2.20830.2281410.18032617X-RAY DIFFRACTION99
2.2083-2.27320.23871360.17832664X-RAY DIFFRACTION100
2.2732-2.34660.16981520.16432576X-RAY DIFFRACTION100
2.3466-2.43040.18331550.16052652X-RAY DIFFRACTION100
2.4304-2.52770.22551380.16522624X-RAY DIFFRACTION100
2.5277-2.64270.19421410.16092628X-RAY DIFFRACTION100
2.6427-2.7820.21341530.16692657X-RAY DIFFRACTION100
2.782-2.95620.1771340.16372659X-RAY DIFFRACTION100
2.9562-3.18430.18541280.16082651X-RAY DIFFRACTION100
3.1843-3.50450.16571410.15452656X-RAY DIFFRACTION99
3.5045-4.0110.15491370.13442645X-RAY DIFFRACTION99
4.011-5.05110.1561420.13192664X-RAY DIFFRACTION98
5.0511-35.29210.19041430.1992767X-RAY DIFFRACTION99

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