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Crystal Structure of Human Glycolate Oxidase in Complex with Glyoxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 HEPES,PEG 600,glyoxylate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.386 α = 90 b = 97.386 β = 90 c = 80.468 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2006-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 30.8 98.8 0.073 11.6 4.57 44625 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 88.8 0.412 2.7 3.08 3990
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GOX 1.65 30.8 44620 2244 98.78 0.183 0.181 0.212 0.2106 RANDOM 13.36
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.834 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_1_deg 6.14 r_scangle_it 3.496 r_scbond_it 2.219 r_angle_refined_deg 1.35 r_mcangle_it 1.208 r_mcbond_it 0.844 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.834 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_1_deg 6.14 r_scangle_it 3.496 r_scbond_it 2.219 r_angle_refined_deg 1.35 r_mcangle_it 1.208 r_mcbond_it 0.844 r_nbtor_refined 0.305 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.11 r_symmetry_hbond_refined 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2801 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 36
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction