3KP9

Structure of a bacterial homolog of vitamin K epoxide reductase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION729815% PEG1000, 0.2M magnesium chloride, pH 7, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
5.8578.985

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.942α = 90
b = 136.942β = 90
c = 68.48γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 3152008-11-20MMIR
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.00718APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.6118.699.18650857211

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT3.644.83771485599.050.256270.251140.305RANDOM55.017
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]
2.741.372.74-4.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.577
r_dihedral_angle_3_deg22.001
r_dihedral_angle_4_deg17.564
r_dihedral_angle_1_deg7.79
r_angle_refined_deg1.492
r_scangle_it1.443
r_scbond_it0.847
r_mcangle_it0.692
r_mcbond_it0.355
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.577
r_dihedral_angle_3_deg22.001
r_dihedral_angle_4_deg17.564
r_dihedral_angle_1_deg7.79
r_angle_refined_deg1.492
r_scangle_it1.443
r_scbond_it0.847
r_mcangle_it0.692
r_mcbond_it0.355
r_chiral_restr0.106
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1963
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement