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Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 0.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.93 75.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.985 α = 90 b = 161.985 β = 90 c = 245.18 γ = 90
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 ADSC QUANTUM 315r 2012-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
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 2.3 50 99.94 0.12 23.5 7.3 137559
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 2.31 2.39 0.54
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 6LD7 2.31 40.61 131279 6941 99.95 0.167 0.1655 0.1707 0.1945 0.196 RANDOM 32.296
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 r_dihedral_angle_2_deg 31.965 r_dihedral_angle_4_deg 21.729 r_dihedral_angle_3_deg 18.047 r_dihedral_angle_1_deg 7.376 r_angle_refined_deg 1.901 r_angle_other_deg 1.459 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.965 r_dihedral_angle_4_deg 21.729 r_dihedral_angle_3_deg 18.047 r_dihedral_angle_1_deg 7.376 r_angle_refined_deg 1.901 r_angle_other_deg 1.459 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11491 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASES phasing