7ZS4

F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HIH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2912 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 30% PEG 550 (v/v) and 0.1 M MES, pH 6.5. Cryoprotection in ML plus 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.856.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.674α = 90
b = 105.674β = 90
c = 105.674γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.7574.721000.0730.02817.46.640057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.781002.2840.8680.66.8

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 REPLACEMENTTHROUGHOUT6HIH1.7574.7138496199699.980.18750.18620.2131RANDOM33.055
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.65
r_dihedral_angle_4_deg18.797
r_dihedral_angle_3_deg11.707
r_dihedral_angle_1_deg7.2
r_angle_refined_deg2.094
r_angle_other_deg1.401
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.65
r_dihedral_angle_4_deg18.797
r_dihedral_angle_3_deg11.707
r_dihedral_angle_1_deg7.2
r_angle_refined_deg2.094
r_angle_other_deg1.401
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2099
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms107

Software

Software
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
REFMACphasing