2VR2

Human Dihydropyrimidinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M HEPES PH 7.5, 70% MPD
Crystal Properties
Matthews coefficientSolvent content
2.3347.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.65α = 90
b = 89.65β = 90
c = 219.1γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL ZERODUR MIRROR2007-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.820990.0926.6317.23134252
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)
12.82.999.10.666.0117.94

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2FTW2.819.951274268299.40.2030.20.251RANDOM59.65
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]
4.452.234.45-6.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.054
r_dihedral_angle_3_deg15.41
r_dihedral_angle_4_deg14.995
r_dihedral_angle_1_deg4.911
r_angle_refined_deg0.945
r_scangle_it0.541
r_scbond_it0.321
r_nbtor_refined0.296
r_mcangle_it0.273
r_nbd_refined0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.054
r_dihedral_angle_3_deg15.41
r_dihedral_angle_4_deg14.995
r_dihedral_angle_1_deg4.911
r_angle_refined_deg0.945
r_scangle_it0.541
r_scbond_it0.321
r_nbtor_refined0.296
r_mcangle_it0.273
r_nbd_refined0.17
r_mcbond_it0.152
r_symmetry_vdw_refined0.144
r_xyhbond_nbd_refined0.102
r_symmetry_hbond_refined0.098
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3693
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing