2BGV

X-ray structure of ferric cytochrome c-550 from Paracoccus versutus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherSTRUCTURE OF M100K CYTOCHROME C-550

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
193.2 M AMMONIUM SULFATE, 0.1 M BICINE PH 9
Crystal Properties
Matthews coefficientSolvent content
1.832.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.102α = 90
b = 57.102β = 90
c = 66.616γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMAR scanner 345 mm plateMIRRORS2003-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR78

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
11.854599.90.1320.514.598982
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)
11.851.9297.70.331.246.6

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 REPLACEMENTTHROUGHOUTSTRUCTURE OF M100K CYTOCHROME C-5501.943.44869043699.70.160.1580.170.1910.19RANDOM20.45
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]
-0.25-0.250.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.952
r_dihedral_angle_3_deg14.98
r_dihedral_angle_4_deg11.972
r_dihedral_angle_1_deg5.869
r_scangle_it3.549
r_mcangle_it3.349
r_mcbond_it3.112
r_scbond_it2.651
r_angle_refined_deg1.158
r_angle_other_deg0.721
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms900
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms43

Software

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