4D4N

Nitrosyl complex of the D121A variant of cytochrome c prime from Alcaligenes xylosoxidans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULFATE, HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7655.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.756α = 90
b = 53.756β = 90
c = 180.023γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-03-20MSINGLE 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
11.459.397.50.0812.15.727816
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)
11.451.597.10.732.56

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.4546.5526396139997.670.16130.159190.20074RANDOM25.419
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]
-0.61-0.31-0.611.99
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.747
r_dihedral_angle_2_deg32.435
r_sphericity_bonded16.342
r_dihedral_angle_4_deg15.37
r_dihedral_angle_3_deg14.209
r_rigid_bond_restr5.515
r_scbond_it5.055
r_dihedral_angle_1_deg4.962
r_mcangle_it3.855
r_mcbond_it3.445
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.747
r_dihedral_angle_2_deg32.435
r_sphericity_bonded16.342
r_dihedral_angle_4_deg15.37
r_dihedral_angle_3_deg14.209
r_rigid_bond_restr5.515
r_scbond_it5.055
r_dihedral_angle_1_deg4.962
r_mcangle_it3.855
r_mcbond_it3.445
r_mcbond_other3.411
r_angle_refined_deg2.259
r_angle_other_deg1.844
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.009
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 Atoms937
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling