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Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JX4 PDB ENTRY 4JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH CRYSTALLIZATION UNDER OIL 6 298 11% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 345 mM Tetramethylammonium chloride, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.641 α = 90 b = 157.828 β = 90 c = 244.953 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-D 1.12706 APS 21-ID-D
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 2.4 50 99.8 0.069 25.7 7.2 128300 128103 -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 2.4 2.46 99.8 0.405 5.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4JX4 2.4 49.66 121746 6448 99.62 0.18568 0.18369 0.1888 0.22319 0.2244 RANDOM 62.797
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] 5.58 -1.04 -4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 18.638 r_dihedral_angle_3_deg 14.923 r_dihedral_angle_1_deg 5.802 r_long_range_B_refined 4.13 r_long_range_B_other 4.127 r_scangle_other 2.592 r_mcangle_it 2.563 r_mcangle_other 2.563 r_scbond_it 1.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 18.638 r_dihedral_angle_3_deg 14.923 r_dihedral_angle_1_deg 5.802 r_long_range_B_refined 4.13 r_long_range_B_other 4.127 r_scangle_other 2.592 r_mcangle_it 2.563 r_mcangle_other 2.563 r_scbond_it 1.676 r_scbond_other 1.676 r_mcbond_it 1.615 r_mcbond_other 1.615 r_angle_refined_deg 1.385 r_angle_other_deg 0.801 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17838 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 206
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling