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Crystal Structure of Cystathionine gamma-synthase MetB (Cgs) from Mycobacterium ulcerans Agy99 bound to HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QI6 PDB ENTRY 3QI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 25.5% PEG4000, 15% glycerol, 170 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.963 α = 90 b = 106.326 β = 113.72 c = 100.548 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 ADSC QUANTUM 315r 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.65 29.231 98 0.093 7.5 3.8 186847 182652
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 1.65 1.71 96.5 0.443 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3QI6 1.65 29.231 173473 9180 97.73 0.15002 0.14839 0.18077 0.1876 RANDOM 12.438
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] -0.54 -0.13 0.78 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.818 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.971 r_scbond_it 3.16 r_mcangle_it 2.159 r_angle_refined_deg 2.157 r_mcbond_it 1.35 r_angle_other_deg 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.818 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.971 r_scbond_it 3.16 r_mcangle_it 2.159 r_angle_refined_deg 2.157 r_mcbond_it 1.35 r_angle_other_deg 1.171 r_mcbond_other 0.476 r_chiral_restr 0.147 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10936 Nucleic Acid Atoms Solvent Atoms 1487 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing