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The structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DT7
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, 8MM MNCL2, 10mM GTP
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.59 α = 90 b = 118.809 β = 109.3 c = 60.508 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 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9 SSRL BL7-1
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 1.49 100 99.9 0.088 13 6.1 95906
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 1.5 1.55 99.9 0.512 5.9 9625
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3DT7 1.49 34.34 90947 4787 99.1 0.2056 0.2044 0.2102 0.2286 0.2328 RANDOM 23.33
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] -0.39 -0.16 -0.01 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.177 r_dihedral_angle_4_deg 16.611 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_1_deg 6.398 r_angle_refined_deg 1.621 r_angle_other_deg 0.968 r_mcangle_it 0.374 r_mcbond_it 0.209 r_mcbond_other 0.209 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.177 r_dihedral_angle_4_deg 16.611 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_1_deg 6.398 r_angle_refined_deg 1.621 r_angle_other_deg 0.968 r_mcangle_it 0.374 r_mcbond_it 0.209 r_mcbond_other 0.209 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4811 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing