5AWI | pdb_00005awi

Domain-swapped cytochrome cb562 dimer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BC5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527725% PEG MME 350, 6 mM ZnSO4, 750 mM MES buffer
Crystal Properties
Matthews coefficientSolvent content
3.0259.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.608α = 90
b = 94.608β = 90
c = 94.608γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

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
11.85201000.0616916.424682
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)
11.851.881000.5946.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2BC51.8519.312315411991000.181250.179970.190.204870.21RANDOM36.971
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]
-5.6220.61-7.0521.13-12.38-15.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.626
r_dihedral_angle_3_deg14.585
r_dihedral_angle_4_deg9.727
r_dihedral_angle_1_deg4.579
r_long_range_B_refined3.323
r_long_range_B_other3.319
r_scangle_other1.409
r_mcangle_other1.364
r_mcangle_it1.363
r_angle_refined_deg1.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.626
r_dihedral_angle_3_deg14.585
r_dihedral_angle_4_deg9.727
r_dihedral_angle_1_deg4.579
r_long_range_B_refined3.323
r_long_range_B_other3.319
r_scangle_other1.409
r_mcangle_other1.364
r_mcangle_it1.363
r_angle_refined_deg1.176
r_scbond_it1.093
r_angle_other_deg0.928
r_scbond_other0.889
r_mcbond_it0.823
r_mcbond_other0.82
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms1630
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing