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Crystal Structure of a Glyoxylate/Hydroxypyruvate reductase from Homo sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GDH 1GDH, 1WWK as a basis of 2-member ensemble experimental model PDB 1WWK 1GDH, 1WWK as a basis of 2-member ensemble
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PROTEIN SOLUTION (10 MG/ML PROTEIN,
0.050 M SODIUM CHLORIDE,
0.0003 M TCEP, 0.005 MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE
WELL SOLUTION (12% PEG 3350, 0.10 M MOPS PH 7). Crystal was
cryo-protected with 15% PEG 3350, 0.10 M PIPES PH 6.5 and a final
concentration of 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.996 α = 90 b = 66.436 β = 98.59 c = 148.774 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97928 APS 23-ID-D
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 2.45 49.326 93.3 0.157 7.087 6.2 50144
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 2.45 2.51 80.3 0.504 2.261 4.8 2832
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 (All) 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 1GDH, 1WWK as a basis of 2-member ensemble 2.45 49.326 50129 2551 93.114 0.21 0.2072 0.2136 0.2643 0.2657 RANDOM 8.853
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] -0.69 -1.165 -0.427 0.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_4_deg 22.585 r_dihedral_angle_3_deg 17.416 r_dihedral_angle_1_deg 6.344 r_scangle_it 5.649 r_scbond_it 3.723 r_mcangle_it 1.682 r_angle_refined_deg 1.59 r_mcbond_it 0.951 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_4_deg 22.585 r_dihedral_angle_3_deg 17.416 r_dihedral_angle_1_deg 6.344 r_scangle_it 5.649 r_scbond_it 3.723 r_mcangle_it 1.682 r_angle_refined_deg 1.59 r_mcbond_it 0.951 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.255 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9768 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction