2YKZ

RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULPHATE, TRIS PH 7.5 .
Crystal Properties
Matthews coefficientSolvent content
2.7455.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.47α = 90
b = 53.47β = 90
c = 181.19γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2008-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
10.841992.20.0410.5612893010.1
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)
10.840.972.80.782.125.3

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 DIFFRACTIONOTHERTHROUGHOUTNONE0.8419.51123627515192.20.106150.105740.11602RANDOM10.3
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]
-0.16-0.08-0.160.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.942
r_dihedral_angle_4_deg26.413
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg5.189
r_scangle_it4.135
r_scbond_it3.197
r_mcangle_it2.307
r_angle_refined_deg2.038
r_mcbond_it1.562
r_rigid_bond_restr1.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.942
r_dihedral_angle_4_deg26.413
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg5.189
r_scangle_it4.135
r_scbond_it3.197
r_mcangle_it2.307
r_angle_refined_deg2.038
r_mcbond_it1.562
r_rigid_bond_restr1.324
r_angle_other_deg0.937
r_mcbond_other0.429
r_chiral_restr0.108
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_gen_planes_other0.005
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_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms952
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling