4CJG

Spectroscopically validated structure of the 5 coordinate proximal NO adduct of cytochrome c prime from Alcaligenes xylosoxidans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULPHATE, HEPES PG 7.5
Crystal Properties
Matthews coefficientSolvent content
2.856.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.621α = 90
b = 53.621β = 90
c = 180.259γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.264596.70.0513.25.240695
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)
11.261.2896.70.672.14.8

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.2646.4438619207195.520.163220.161610.19465RANDOM15.903
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]
-0.45-0.22-0.451.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.647
r_sphericity_free25.587
r_dihedral_angle_3_deg14.632
r_dihedral_angle_4_deg13.871
r_sphericity_bonded12.706
r_rigid_bond_restr6.199
r_dihedral_angle_1_deg5.383
r_angle_refined_deg2.25
r_scbond_it2.237
r_mcangle_it2.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.647
r_sphericity_free25.587
r_dihedral_angle_3_deg14.632
r_dihedral_angle_4_deg13.871
r_sphericity_bonded12.706
r_rigid_bond_restr6.199
r_dihedral_angle_1_deg5.383
r_angle_refined_deg2.25
r_scbond_it2.237
r_mcangle_it2.187
r_mcbond_it1.77
r_mcbond_other1.735
r_angle_other_deg1.027
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms949
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling