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Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QF7 CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH CRYSTALLIZATION UNDER OIL 6 298 11.3 (w/v) PEG 8000, 99 mM BisTris (pH 6.0), 346 mM Tetramethylammonium chloride , BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 58.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.13 α = 90 b = 157.253 β = 90 c = 245.32 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD 2012-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.55 50 99.8 0.085 24 7.2 107850 107658 -3
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 2.55 2.59 99.9 0.444 4.4 7.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7 2.55 46.88 102382 5384 99.46 0.18888 0.1866 0.2321 0.2388 RANDOM 68.802
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] 7.93 -2.87 -5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.213 r_dihedral_angle_4_deg 21.263 r_dihedral_angle_3_deg 16.298 r_dihedral_angle_1_deg 6.117 r_mcangle_it 2.693 r_scbond_it 2.2 r_mcbond_it 1.699 r_angle_refined_deg 1.513 r_chiral_restr 0.097 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.213 r_dihedral_angle_4_deg 21.263 r_dihedral_angle_3_deg 16.298 r_dihedral_angle_1_deg 6.117 r_mcangle_it 2.693 r_scbond_it 2.2 r_mcbond_it 1.699 r_angle_refined_deg 1.513 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17668 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 48
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling