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The Structure of rat cytosolic PEPCK in complex with 3-phosphonopropionate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.294 α = 90 b = 119.397 β = 108.66 c = 60.762 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 118 IMAGE PLATE RIGAKU RAXIS IV++ BLUE OSMIC Confocal MIRRORS 2007-06-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.9 100 97.2 0.092 14.9 7 46838
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 1.9 1.97 84.2 0.653 5.5 4065
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.9 33.98 46794 2377 97.11 0.189 0.187 0.1843 0.233 0.2283 RANDOM 15.395
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] 0.03 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.195 r_dihedral_angle_4_deg 15.192 r_dihedral_angle_3_deg 15.043 r_dihedral_angle_1_deg 5.749 r_scangle_it 1.711 r_angle_refined_deg 1.112 r_scbond_it 1.038 r_mcangle_it 0.669 r_mcbond_it 0.362 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.195 r_dihedral_angle_4_deg 15.192 r_dihedral_angle_3_deg 15.043 r_dihedral_angle_1_deg 5.749 r_scangle_it 1.711 r_angle_refined_deg 1.112 r_scbond_it 1.038 r_mcangle_it 0.669 r_mcbond_it 0.362 r_nbtor_refined 0.301 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.16 r_metal_ion_refined 0.136 r_symmetry_hbond_refined 0.121 r_xyhbond_nbd_refined 0.12 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 4819 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection