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Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 12% PEG3350, 0.1M Bis-Tris, 0.1M Mg Formate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.946 α = 90 b = 105.394 β = 90 c = 199.748 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 MARMOSAIC 225 mm CCD A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium. 2007-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 50 99.8 0.081 0.078 23.24 6.9 115364 114964 14.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 97.9 0.354 0.317 4.09 5.4 11187
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2ZDG 1.9 47.9 111841 11204 96.9 0.207 0.207 0.207 0.239 0.2377 RANDOM 24.1
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] -5.01 3.55 1.46
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.87 c_scbond_it 1.94 c_mcangle_it 1.91 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.94 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9711 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 127
Software Software Software Name Purpose CNS refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing