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Pantoate-beta-alanine ligase from Yersinia pestis in complex with pantoate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.1 M Bis-Tris, 20% PEG-5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.73 α = 100.67 b = 77.054 β = 95.33 c = 98.757 γ = 94.43
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 2010-11-21 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 1.58 36.7 87.4 0.042 17.2 2.1 153768 153768 29.7
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) 1.58 1.61 41.7 0.267 2.94 1.9 3691
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 3Q10 1.58 36.69 153765 153765 7730 87.24 0.1519 0.1519 0.1496 0.1535 0.1951 0.1974 RANDOM 28.2763
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] -0.8 -0.04 0.26 -0.93 0.92 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.282 r_dihedral_angle_4_deg 16.07 r_dihedral_angle_3_deg 13.543 r_scangle_it 6.189 r_dihedral_angle_1_deg 5.74 r_scbond_it 4.118 r_mcangle_it 2.758 r_mcbond_it 1.766 r_rigid_bond_restr 1.676 r_angle_refined_deg 1.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.282 r_dihedral_angle_4_deg 16.07 r_dihedral_angle_3_deg 13.543 r_scangle_it 6.189 r_dihedral_angle_1_deg 5.74 r_scbond_it 4.118 r_mcangle_it 2.758 r_mcbond_it 1.766 r_rigid_bond_restr 1.676 r_angle_refined_deg 1.668 r_angle_other_deg 0.984 r_mcbond_other 0.562 r_chiral_restr 0.225 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8920 Nucleic Acid Atoms Solvent Atoms 1154 Heterogen Atoms 42
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