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D-alanine--D-alanine ligase from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M magnesium chloride, 0.1 M sodium cacodylate, 50% PEG-200, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.637 α = 90 b = 100.637 β = 90 c = 110.304 γ = 120
Symmetry Space Group P 31 2 1
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 SBC-3 2008-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 2.7 31.6 99.9 0.091 7.9 9.9 18282 18282 70.5
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 2.7 2.75 100 0.89 2.43 10.1 907
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 (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 1IOW 2.69 31.7 18203 18203 927 99.5 0.2094 0.2053 0.2023 0.2888 0.2837 RANDOM 61.8005
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] -3.64 -1.82 -3.64 5.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 20.748 r_dihedral_angle_3_deg 19.73 r_dihedral_angle_1_deg 6.445 r_angle_refined_deg 1.871 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4399 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 17
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