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Crystal structure of D-cycloserine synthetase DcsG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 1.0 M potassium sodium L-tartrate, 0.1 M Tris-HCl buffer (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.45 α = 90 b = 120.73 β = 101.01 c = 102.81 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-225 2015-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.97864 SPring-8 BL38B1
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 2.32 100 95.3 0.117 10.1 3.6 55347 20.1
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 2.32 2.4 82.4 0.447 1.8 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.32 29.76 2 55347 2816 94.6 0.195 0.195 0.1969 0.251 0.2518 RANDOM 25.1
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] 7.06 -4.64 -4.56 -2.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.17 c_scbond_it 2.25 c_mcangle_it 2.05 c_angle_deg 1.3 c_mcbond_it 1.27 c_improper_angle_d 0.82 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.17 c_scbond_it 2.25 c_mcangle_it 2.05 c_angle_deg 1.3 c_mcbond_it 1.27 c_improper_angle_d 0.82 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9184 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 217
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling SHARP phasing