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Pantoate-beta-alanine ligase from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.1 M Bis-Tris, 25% PEG-3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.809 α = 101.33 b = 77.241 β = 94.91 c = 98.462 γ = 94.37
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 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.83 33.1 96.8 0.044 11.6 2.6 109573 109573 34.7
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) 1.83 1.86 94.4 0.458 2.08 2.4 5387
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 1IHO 1.83 33.1 109539 109539 5527 96.43 0.1755 0.1755 0.1736 0.1876 0.2108 0.2269 RANDOM 36.882
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] -1.57 -0.11 0.02 -1.23 0.95 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.704 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 15.083 r_dihedral_angle_1_deg 5.824 r_scangle_it 3.758 r_scbond_it 2.36 r_angle_refined_deg 1.593 r_mcangle_it 1.536 r_angle_other_deg 0.96 r_mcbond_it 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.704 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 15.083 r_dihedral_angle_1_deg 5.824 r_scangle_it 3.758 r_scbond_it 2.36 r_angle_refined_deg 1.593 r_mcangle_it 1.536 r_angle_other_deg 0.96 r_mcbond_it 0.902 r_mcbond_other 0.287 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8261 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 128
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing