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Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin
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 14% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.88 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.87 α = 90 b = 157.123 β = 90 c = 244.714 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 225 mm CCD 2011-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.26 50 98.3 0.084 20.6 7.1 148360 145868 -3 34.4
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 2.26 2.3 94.7 0.444 3.4 6.8
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 2.26 43.75 140726 7444 97.97 0.17837 0.17635 0.1841 0.21628 0.2172 RANDOM 50.934
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] 4.52 -1.78 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 19.813 r_dihedral_angle_3_deg 15.782 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.794 r_long_range_B_other 5.794 r_scangle_other 2.931 r_mcangle_it 2.462 r_mcangle_other 2.462 r_scbond_it 2.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 19.813 r_dihedral_angle_3_deg 15.782 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.794 r_long_range_B_other 5.794 r_scangle_other 2.931 r_mcangle_it 2.462 r_mcangle_other 2.462 r_scbond_it 2.241 r_scbond_other 2.241 r_angle_refined_deg 1.836 r_mcbond_it 1.656 r_mcbond_other 1.655 r_angle_other_deg 0.896 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 17888 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 111
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling