5JP7

Ferrous Leu 16 Val mutant of cytochrome c prime from Alcaligenes xylosoxidans


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52942.2 M Ammonium sulfate 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
255.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.309α = 90
b = 53.309β = 90
c = 180.722γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

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
11.2546.299.90.03218543208
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)
11.251.3299.90.7724.6

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-VALUE2YLI1.26103643140471000.17320.215RANDOM24.4398
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_d313
s_zero_chiral_vol58
s_non_zero_chiral_vol1
s_approx_iso_adps0.122
s_similar_adp_cmpnt0.049
s_anti_bump_dis_restr0.027
s_bond_d0.012
s_from_restr_planes0.003
s_similar_dist
s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms948
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms43

Software

Software
Software NamePurpose
SCALAdata scaling
SHELXLrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction