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The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop vapor diffusion 7.4 298 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, hanging drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.154 α = 90 b = 119.683 β = 107.05 c = 86.849 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2007-12-04 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9 SSRL BL11-1
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 1.3 100 97.9 0.118 8.5 10.5 291304
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 1.3 1.35 87.4 0.783 6.4 25897
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 1.3 28.83 291113 14703 97.69 0.169 0.168 0.1712 0.193 0.1932 RANDOM 11.645
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 -0.03 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 6.802 r_scangle_it 3.557 r_scbond_it 2.214 r_angle_refined_deg 1.513 r_mcangle_it 1.475 r_mcbond_it 0.856 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 6.802 r_scangle_it 3.557 r_scbond_it 2.214 r_angle_refined_deg 1.513 r_mcangle_it 1.475 r_mcbond_it 0.856 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9684 Nucleic Acid Atoms Solvent Atoms 1544 Heterogen Atoms 119
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling