8BRL

Room temperature crystal structure of cytochrome c' from Hydrogenophilus thermoluteolus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B3I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529330% PEG 8000, 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.536α = 90
b = 83.536β = 90
c = 88.566γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER2 X 4M2022-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE VMXi0.7749DiamondVMXi

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
11.8856.091000.4590.4690.0930.9957.922.315440
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)
11.881.911005.4965.6831.4010.2580.615.4

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 REPLACEMENTTHROUGHOUT5B3I1.8856.091462077799.90.179180.177910.20314RANDOM31.553
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.968
r_dihedral_angle_4_deg21.823
r_dihedral_angle_3_deg17.295
r_long_range_B_refined9.379
r_long_range_B_other9.35
r_scangle_other7.873
r_dihedral_angle_1_deg5.893
r_scbond_it5.247
r_scbond_other5.095
r_mcangle_it4.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.968
r_dihedral_angle_4_deg21.823
r_dihedral_angle_3_deg17.295
r_long_range_B_refined9.379
r_long_range_B_other9.35
r_scangle_other7.873
r_dihedral_angle_1_deg5.893
r_scbond_it5.247
r_scbond_other5.095
r_mcangle_it4.162
r_mcangle_other4.159
r_mcbond_it2.763
r_mcbond_other2.762
r_angle_refined_deg2.32
r_angle_other_deg1.481
r_chiral_restr0.158
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1029
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing