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The Crystal Structure of Ornithine Acetyltransferase from Mycobacterium tuberculosis (Rv1653) at 1.7 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VZ6 PDB entry 1VZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Protein Concentration 13.5 mg/mL in 2.5 mM HEPES pH 7.5, precipitant 0.02 M MgCl2, 22% polyacrylic acid 5100 in 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.14 α = 90 b = 99.699 β = 90 c = 155.245 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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2008-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115872 ALS 8.3.1
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 1.7 50 95.6 0.077 13.4 3.5 98245 98245
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) 1.7 1.76 96.5 0.321 4.1 3.5 9834
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1VZ6 1.7 35.9 93276 93276 4899 95 0.20637 0.20637 0.2044 0.2018 0.24371 0.2406 RANDOM 22.36
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] 0.02 -0.87 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.919 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.994 r_scangle_it 3.658 r_scbond_it 2.251 r_angle_refined_deg 1.364 r_mcangle_it 1.277 r_mcbond_it 0.75 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.919 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.994 r_scangle_it 3.658 r_scbond_it 2.251 r_angle_refined_deg 1.364 r_mcangle_it 1.277 r_mcbond_it 0.75 r_chiral_restr 0.091 r_bond_refined_d 0.012 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5605 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 35
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling