2VLZ

Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GJNPDB ENTRY 1GJN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 5.2)
Crystal Properties
Matthews coefficientSolvent content
1.4816.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.804α = 90
b = 28.714β = 105.82
c = 35.452γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2007-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3834.1699.50.066.413.5920072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.581000.441.452.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GJN1.526.871904397399.30.1640.1620.19RANDOM17.9
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.170.170.20.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.193
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg12.525
r_dihedral_angle_1_deg4.371
r_scangle_it2.856
r_scbond_it1.878
r_angle_refined_deg1.166
r_mcangle_it1.107
r_mcbond_it0.668
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.193
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg12.525
r_dihedral_angle_1_deg4.371
r_scangle_it2.856
r_scbond_it1.878
r_angle_refined_deg1.166
r_mcangle_it1.107
r_mcbond_it0.668
r_nbtor_refined0.304
r_nbd_refined0.198
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.129
r_chiral_restr0.07
r_bond_refined_d0.055
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1199
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing