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Structure of the carboxyl transferase domain Y628A 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 6 298 11.7% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 200 mM Tetramethylammonium chloride, 3% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 58.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.809 α = 90 b = 157.28 β = 90 c = 245.885 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 2012-06-10 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 2.78 50 99.9 0.074 26.3 7.2 83991 83911 -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 2.78 2.83 99.6 0.426 4.3 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 CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7 2.78 50 79718 4189 99.8 0.21147 0.20894 0.2108 0.25844 0.2592 RANDOM 72.618
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] 8.91 -2.29 -6.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 17.043 r_dihedral_angle_1_deg 5.908 r_angle_refined_deg 1.384 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 17.043 r_dihedral_angle_1_deg 5.908 r_angle_refined_deg 1.384 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 17245 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 26
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling