5JVE

L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52942.2M Ammonium sulfate, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0255.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.52α = 90
b = 53.52β = 90
c = 179.682γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.144.898.70.0640.9989.65.561939
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)
11.11.1294.80.6521.54.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2YLI1.12105199642.50.1530.181RANDOM18.1983
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
s_angle_d325
s_zero_chiral_vol53
s_non_zero_chiral_vol8
s_approx_iso_adps0.121
s_similar_adp_cmpnt0.041
s_anti_bump_dis_restr0.035
s_bond_d0.015
s_from_restr_planes0.004
s_similar_dist
s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms940
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms43

Software

Software
Software NamePurpose
Aimlessdata scaling
SHELXDEphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing