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Rat cytosolic PEPCK, in complex with manganese ion.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 12-30% PEG 3350, 0.1M HEPES pH 7.4, 10 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.448 α = 90 b = 119.046 β = 109.59 c = 60.599 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++ Blue osmic confocal 2007-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 1.8 50 97.9 0.08 13.1 7.3 53469 53469 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 93.2 0.546 5.5 5077
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KHG 1.8 24.26 53450 53450 2721 97.83 0.18 0.18 0.178 0.1766 0.213 0.2119 RANDOM 20.668
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] 0.23 0.05 -0.15 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_1_deg 5.466 r_scangle_it 1.847 r_scbond_it 1.106 r_angle_refined_deg 1.079 r_mcangle_it 0.731 r_mcbond_it 0.395 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_1_deg 5.466 r_scangle_it 1.847 r_scbond_it 1.106 r_angle_refined_deg 1.079 r_mcangle_it 0.731 r_mcbond_it 0.395 r_nbtor_refined 0.302 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.127 r_metal_ion_refined 0.111 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4819 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing