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The structure of rat cytosolic PEPCK variant E89A in complex with oxalic acid and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DT4
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 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.699 α = 90 b = 119.313 β = 107.95 c = 60.821 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 315r 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97 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 1.6 100 98.7 0.069 16.2 5.9 80122
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 1.6 1.66 91.5 0.308 5.2 7417
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 3DT4 1.6 59.66 76005 4009 98.53 0.2068 0.2048 0.2117 0.2428 0.2478 RANDOM 22.103
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.767 r_mcangle_it 2.288 r_angle_refined_deg 1.436 r_mcbond_it 1.377 r_mcbond_other 1.377 r_angle_other_deg 0.883 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.767 r_mcangle_it 2.288 r_angle_refined_deg 1.436 r_mcbond_it 1.377 r_mcbond_other 1.377 r_angle_other_deg 0.883 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4802 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing