1GKQ

D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group P212121


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GKP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530% (W/V) PEG 6000, 100 MM CACODYLATE/HCL PH 6.5, 200 MM SODIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.861

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 161.5β = 90
c = 168.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray283IMAGE PLATEMAC SCIENCE DIP-2030H1997-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
12.6251000.117125.97039438.8
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)
12.62.6999.90.3634.95.7

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 REPLACEMENTTHROUGHOUT1GKP2.62570394355699.80.18760.18760.2109RANDOM28.3
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]
2.335-6.5644.23
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_scangle_it3.238
c_scbond_it2.158
c_mcangle_it1.949
c_angle_deg1.36
c_mcbond_it1.178
c_improper_angle_d0.84
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_scangle_it3.238
c_scbond_it2.158
c_mcangle_it1.949
c_angle_deg1.36
c_mcbond_it1.178
c_improper_angle_d0.84
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14304
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms8

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing