7ZVZ

Cytochrome c prime beta from Methylococcus capsulatus (Bath): Chemically Reduced Ferrous Form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29115 mg/ml protein mixed with 10 mM ZnSO4, 35% PEG 550, 100 mM MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.2762.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.56α = 90
b = 105.56β = 90
c = 105.56γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.6843.091000.0440.0480.018124.26.744860
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.721001.3151.4240.5410.5516.8

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 REPLACEMENTTHROUGHOUT6HIH1.6837.3542598221699.950.19370.19210.2283RANDOM31.401
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_deg31.195
r_dihedral_angle_4_deg20.063
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg6.894
r_angle_refined_deg2.322
r_angle_other_deg1.417
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_gen_planes_other0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.195
r_dihedral_angle_4_deg20.063
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg6.894
r_angle_refined_deg2.322
r_angle_other_deg1.417
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_gen_planes_other0.014
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms105

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
REFMACphasing