5NC0

The 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298AMMONIUM SULPHATE, TRIS PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6753.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.43α = 90
b = 52.43β = 90
c = 183.25γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.78720SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
10.9144.0799.50.0230.99916.18106845
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.910.9393.90.5640.5471.34.4

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 REPLACEMENTTHROUGHOUT2YL70.9144.07101466537899.290.12490.124530.13177RANDOM8.977
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]
-0.15-0.07-0.150.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.774
r_sphericity_free19.653
r_dihedral_angle_4_deg11.307
r_dihedral_angle_3_deg11.017
r_sphericity_bonded6.354
r_rigid_bond_restr5.075
r_dihedral_angle_1_deg4.75
r_long_range_B_refined2.578
r_long_range_B_other2.577
r_angle_refined_deg2.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.774
r_sphericity_free19.653
r_dihedral_angle_4_deg11.307
r_dihedral_angle_3_deg11.017
r_sphericity_bonded6.354
r_rigid_bond_restr5.075
r_dihedral_angle_1_deg4.75
r_long_range_B_refined2.578
r_long_range_B_other2.577
r_angle_refined_deg2.471
r_scangle_other1.816
r_scbond_it1.53
r_scbond_other1.53
r_angle_other_deg1.075
r_mcangle_other0.984
r_mcangle_it0.976
r_mcbond_it0.716
r_mcbond_other0.623
r_chiral_restr0.096
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms936
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing