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Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase Bound to Pyruvate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 3350, KSCN, Bis tris Propane, TCEP, Ethelyene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.75 74.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.23 α = 90 b = 141.23 β = 90 c = 108.388 γ = 120
Symmetry Space Group P 64 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 IMAGE PLATE RIGAKU RAXIS IV 2009-07-29 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 1.97 35.17 99.9 0.05 20.8 13.82 45370
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 1.97 2.04 100 0.354 5.7 12.3 4465
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.97 34.648 2 45315 2287 99.69 0.1973 0.1963 0.1913 0.2159 0.2132 RANDOM 29.8862
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] -0.52 -0.26 -0.52 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.151 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 14.222 r_dihedral_angle_1_deg 5.712 r_scangle_it 3.771 r_scbond_it 2.277 r_angle_refined_deg 1.429 r_mcangle_it 1.327 r_mcbond_it 0.707 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.151 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 14.222 r_dihedral_angle_1_deg 5.712 r_scangle_it 3.771 r_scbond_it 2.277 r_angle_refined_deg 1.429 r_mcangle_it 1.327 r_mcbond_it 0.707 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 25
Software Software Software Name Purpose d*TREK data scaling PHASER phasing SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction