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Rat cytosolic PEPCK in complex with oxaloacetic acid.
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, 10 mM MnCl2, 0.1M HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.218 α = 90 b = 119.34 β = 108.71 c = 60.808 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 1.8 100 89.3 0.078 12.2 7 50217 50217 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 1.8 1.86 46.4 0.516 5.5 2583
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 (All) 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 2QEW 1.8 24.48 50199 50199 2554 89.27 0.195 0.195 0.194 0.228 0.2811 RANDOM 30.508
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] 0.07 0.05 -0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.008 r_dihedral_angle_4_deg 16.875 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_1_deg 5.372 r_scangle_it 1.732 r_angle_refined_deg 1.116 r_scbond_it 1.08 r_mcangle_it 0.618 r_mcbond_it 0.347 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.008 r_dihedral_angle_4_deg 16.875 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_1_deg 5.372 r_scangle_it 1.732 r_angle_refined_deg 1.116 r_scbond_it 1.08 r_mcangle_it 0.618 r_mcbond_it 0.347 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.12 r_metal_ion_refined 0.087 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4762 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 12
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