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Crystal structure analysis of Diaminopimelate decarboxylate (lysA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 oil-batch 4.5 293 40%(v/v) PEG600, 0.1M Acetate, 0.2M MgCl2, pH 4.5, oil-batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.818 α = 90 b = 98.276 β = 90 c = 109.304 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD RIGAKU JUPITER 210 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.97898, 0.90000, 0.97946 SPring-8 BL26B2
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 1.61 50 98.7 0.078 6.8 61468 60672 -3 15.8
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 1.61 1.67 88.6 0.36 5.1 5394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.7 19.96 51251 5184 98.1 0.189 0.189 0.22 RANDOM 20.8
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] -3.44 -1.38 4.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_angle_deg 2.7 c_improper_angle_d 1.97 c_bond_d 0.032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3091 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 16
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing