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Rat cytosolic PEPCK in complex with oxaloacetic acid and GDP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 25% PEG 3350, 0.1M HEPES pH 7.4, 10 mM MnCl2, 10 mM GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.506 α = 90 b = 119.112 β = 107.35 c = 86.71 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 ADSC QUANTUM 315 Bent conical Si-mirror (Rh coated) 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 50 96.6 0.082 9 6.9 142474 2 2
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 80.3 0.693 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2QEW 1.65 33.33 142341 135193 7148 96.45 0.20597 0.20427 0.2027 0.23762 0.235 RANDOM 19.121
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 5.524 r_scangle_it 1.86 r_angle_refined_deg 1.188 r_scbond_it 1.146 r_mcangle_it 0.724 r_mcbond_it 0.401 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 5.524 r_scangle_it 1.86 r_angle_refined_deg 1.188 r_scbond_it 1.146 r_mcangle_it 0.724 r_mcbond_it 0.401 r_nbtor_refined 0.303 r_nbd_refined 0.186 r_metal_ion_refined 0.161 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.113 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9584 Nucleic Acid Atoms Solvent Atoms 1209 Heterogen Atoms 123
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing