5JLI

Nitric oxide complex of the L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YL0 

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
2.7655.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.629α = 90
b = 53.629β = 90
c = 180.523γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-10-27MSINGLE 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
11.5546.4498.80.0730.99911.96.323047
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)
11.551.6398.10.761.96.5

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 REPLACEMENTTHROUGHOUT2yl01.5546.4421801115598.370.17280.17050.2138RANDOM22.068
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]
-0.37-0.19-0.371.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.506
r_sphericity_free27.816
r_dihedral_angle_4_deg19.954
r_sphericity_bonded14.301
r_dihedral_angle_3_deg13.954
r_dihedral_angle_1_deg4.992
r_mcangle_it2.852
r_mcbond_it2.274
r_mcbond_other2.252
r_rigid_bond_restr2.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.506
r_sphericity_free27.816
r_dihedral_angle_4_deg19.954
r_sphericity_bonded14.301
r_dihedral_angle_3_deg13.954
r_dihedral_angle_1_deg4.992
r_mcangle_it2.852
r_mcbond_it2.274
r_mcbond_other2.252
r_rigid_bond_restr2.251
r_angle_refined_deg2.184
r_angle_other_deg1.024
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms955
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction