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Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBQ PDB ENTRY 2DBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M Lithium Sulfate, 0.1M Tris pH 8.5, 25% Polyethylene Glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.052 α = 113.76 b = 85.443 β = 91.17 c = 107.132 γ = 94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 two dimensional focusing mirror 2005-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 50 94 0.058 14.528 2.566 62135 -3 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 74.6 0.288 2.71 2.4 4918
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DBQ 2.61 49.11 62126 6279 93.2 0.218 0.2154 0.284 0.2796 RANDOM 55
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] 16.71 4.4 -11.44 -11.26 -0.23 -5.46
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.62 c_scbond_it 4.14 c_mcangle_it 3.86 c_mcbond_it 2.43 c_angle_deg 1.2 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.62 c_scbond_it 4.14 c_mcangle_it 3.86 c_mcbond_it 2.43 c_angle_deg 1.2 c_improper_angle_d 0.78 c_bond_d 0.006 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 Atoms Number Protein Atoms 16038 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 348
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing