2ZZS

Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GDV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229310mM sodium phosphate buffer (pH 7.0), 0.1M phosphate-citrate (pH 4.2), 0.2M NaCl, 20%(w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.0941.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.949α = 71.5
b = 87.612β = 72.98
c = 103.847γ = 83.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702008-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0000Photon FactoryBL-17A

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
11.82094.50.063235784223962
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8677.90.2050.2314.12.119421

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GDV1.820235784223962118201000.195190.192690.24213RANDOM26.068
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]
-0.260.48-0.16-0.790.041.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.766
r_dihedral_angle_3_deg14.377
r_dihedral_angle_1_deg8.065
r_dihedral_angle_4_deg7.43
r_scangle_it4.072
r_scbond_it2.77
r_angle_refined_deg1.777
r_mcangle_it1.742
r_mcbond_it1.001
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.766
r_dihedral_angle_3_deg14.377
r_dihedral_angle_1_deg8.065
r_dihedral_angle_4_deg7.43
r_scangle_it4.072
r_scbond_it2.77
r_angle_refined_deg1.777
r_mcangle_it1.742
r_mcbond_it1.001
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18378
Nucleic Acid Atoms
Solvent Atoms1624
Heterogen Atoms1400

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling