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Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.7 MALONATE (HAMPTON), PH 7.0. 1 ml of mother liquor was placed in the well of
the crystallization plate and the drop was formed by mixing 1.5 ul of protein solution at 10 mg/ml and 1.5 ul of mother liquor
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.063 α = 90 b = 141.063 β = 90 c = 260.792 γ = 120
Symmetry Space Group P 62 2 2
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 ADSC QUANTUM 315r MIRROR M1 2012-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979637 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 47.97 99.8 0.17 0.062 1 11.7 7.3 103194 -3 29.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.3 1.5 1.88 0.683 0.527 1.4 7.3
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5AOW 2 44.58 97977 5157 99.67 0.1498 0.1484 0.1629 0.1756 0.188 RANDOM 41.333
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] 0.25 0.12 0.25 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 6.22 r_angle_refined_deg 1.521 r_angle_other_deg 0.969 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 6.22 r_angle_refined_deg 1.521 r_angle_other_deg 0.969 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5237 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing