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Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with homolanthionine
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 0.12M Ethylene Glycols Mix, 0.1M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.87 74.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.222 α = 90 b = 161.222 β = 90 c = 244.914 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 2013-04-24 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 2.39 50 96.15 0.083 8.1 7.3 117802
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 2.39 2.48 0.26
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 2.39 47.07 111910 5900 96.19 0.1551 0.1537 0.1619 0.1813 0.1866 RANDOM 29.899
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.776 r_dihedral_angle_4_deg 21.447 r_dihedral_angle_3_deg 18.307 r_dihedral_angle_1_deg 7.441 r_angle_refined_deg 2.427 r_angle_other_deg 1.602 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.776 r_dihedral_angle_4_deg 21.447 r_dihedral_angle_3_deg 18.307 r_dihedral_angle_1_deg 7.441 r_angle_refined_deg 2.427 r_angle_other_deg 1.602 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11484 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASES phasing