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Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate
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 11.3% (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 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.657 α = 90 b = 157.368 β = 90 c = 244.827 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 0.979 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 0.086 21.1 7.3 108391 108188 -3 51.2
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 99.3 0.437 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 PDB ENTRY 4JX4 2.55 48.26 102898 5409 99.4 0.1952 0.19283 0.23951 0.2637 RANDOM 75.346
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] 8.57 -4.64 -3.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 16.028 r_dihedral_angle_1_deg 6.617 r_long_range_B_refined 5.74 r_long_range_B_other 5.738 r_scangle_other 2.634 r_mcangle_it 2.617 r_mcangle_other 2.617 r_scbond_it 2.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 16.028 r_dihedral_angle_1_deg 6.617 r_long_range_B_refined 5.74 r_long_range_B_other 5.738 r_scangle_other 2.634 r_mcangle_it 2.617 r_mcangle_other 2.617 r_scbond_it 2.341 r_scbond_other 2.316 r_mcbond_it 1.658 r_mcbond_other 1.658 r_angle_refined_deg 1.638 r_angle_other_deg 0.869 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 17794 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 48
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling