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COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 AMMONIUM SULFATE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.6 α = 90 b = 51 β = 90 c = 51.2 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 AREA DETECTOR SIEMENS 1995-09-18 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 75 0.067 8.8 11579
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.4 39
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2DLN 2.2 15 3 7591 75 0.156 0.204 10.3
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]
RMS Deviations Key Refinement Restraint Deviation p_staggered_tor 22.5 p_transverse_tor 19.6 p_angle_d 1.1 p_planar_tor 1.1 p_mcangle_it 0.472 p_xyhbond_nbd 0.365 p_scangle_it 0.356 p_multtor_nbd 0.305 p_mcbond_it 0.263 p_singtor_nbd 0.204
RMS Deviations Key Refinement Restraint Deviation p_staggered_tor 22.5 p_transverse_tor 19.6 p_angle_d 1.1 p_planar_tor 1.1 p_mcangle_it 0.472 p_xyhbond_nbd 0.365 p_scangle_it 0.356 p_multtor_nbd 0.305 p_mcbond_it 0.263 p_singtor_nbd 0.204 p_scbond_it 0.197 p_chiral_restr 0.115 p_planar_d 0.019 p_bond_d 0.008 p_plane_restr 0.005 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms 27 Solvent Atoms 263 Heterogen Atoms 17
Software Software Software Name Purpose PROLSQ refinement XENGEN data reduction XENGEN data scaling