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Structure of the H477R variant of rat cytosolic PEPCK in complex with oxalate and GTP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 24 - 34% PEG 3350 and 100mM HEPES, at pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.526 α = 90 b = 119.605 β = 106.83 c = 60.679 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.95 100 98.5 0.106 17.8 5.3 45590
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 1.95 2.02 88.9 0.556 2.9 4113
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 MOLECULAR REPLACEMENT THROUGHOUT 3DT4 1.95 28.37 43263 2294 97.82 0.1857 0.1843 0.1918 0.2124 0.2193 RANDOM 42.083
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] 0.01 -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.738 r_dihedral_angle_4_deg 14.163 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_1_deg 6.176 r_angle_refined_deg 1.292 r_angle_other_deg 0.891 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.738 r_dihedral_angle_4_deg 14.163 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_1_deg 6.176 r_angle_refined_deg 1.292 r_angle_other_deg 0.891 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4870 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction DENZO data reduction