2DBZ

Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DBQPDB ENTRY 2DBQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62930.2M Potassium Sodium Tartrate pH 5.6, 0.1M Sodium Citrate, 2.0M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.7767.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.472α = 90
b = 104.472β = 90
c = 182.079γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210two dimensional focusing mirror2005-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.455099.50.07221.7897.23641156-355.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5499.80.4654.5026.94081

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DBQ2.4545.3137243374790.20.2390.276RANDOM62.7
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]
-7.184.12-7.1814.37
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.3
c_scangle_it8.36
c_scbond_it6.6
c_mcangle_it5.32
c_mcbond_it3.93
c_angle_deg1.5
c_improper_angle_d0.9
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.3
c_scangle_it8.36
c_scbond_it6.6
c_mcangle_it5.32
c_mcbond_it3.93
c_angle_deg1.5
c_improper_angle_d0.9
c_bond_d0.01
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 Atoms5346
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms116

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing