5JRA

Nitric oxide complex of the L16V 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 DROP7.52942.2M Ammonium sulfate 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7455.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.199α = 90
b = 53.199β = 90
c = 180.679γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.3846.0721000.05115.47.632339
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)
11.381.451000.74416.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2YLI1.3846.0730600163399.980.16370.16260.1858RANDOM24.331
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]
-0.21-0.1-0.210.67
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.824
r_dihedral_angle_2_deg34.924
r_dihedral_angle_4_deg22.861
r_dihedral_angle_3_deg15.546
r_sphericity_bonded13.661
r_dihedral_angle_1_deg5.105
r_rigid_bond_restr3.659
r_mcangle_it3.485
r_mcbond_it2.805
r_mcbond_other2.725
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.824
r_dihedral_angle_2_deg34.924
r_dihedral_angle_4_deg22.861
r_dihedral_angle_3_deg15.546
r_sphericity_bonded13.661
r_dihedral_angle_1_deg5.105
r_rigid_bond_restr3.659
r_mcangle_it3.485
r_mcbond_it2.805
r_mcbond_other2.725
r_angle_refined_deg2.366
r_angle_other_deg1.851
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms948
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms70

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing