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Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QEW PDB ENTRY 2QEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 25% PEG 3350, 0.1M HEPES PH 7.4,2 MM
MNCL2, 10MM GTP, 1MM 3-MERCAPTOPICOLINIC ACID, VAPOR DIFFUSION,
HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.407 α = 90 b = 118.742 β = 110.02 c = 60.248 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 FLAT MIRROR (VERTICAL FOCUSING) 2009-04-02 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 1.4 100 94.4 0.058 13.5 7.2 110377
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 1.4 1.45 76.2 0.417 5.7
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 PDB ENTRY 2QEW 1.4 29.16 104796 5550 93.4 0.17 0.168 0.1764 0.197 0.2018 RANDOM 20.04
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 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 6.26 r_angle_refined_deg 1.787 r_angle_other_deg 0.839 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 6.26 r_angle_refined_deg 1.787 r_angle_other_deg 0.839 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4818 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 55
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC refinement