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Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNENI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y7L PDB ENTRY 1Y7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 HEPES, Ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.264 α = 90 b = 112.264 β = 90 c = 45.835 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 130 IMAGE PLATE RIGAKU RAXIS IV++ 2009-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.7 22.08 97.3 0.033 28.1 3.3 29196 29196
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) 1.7 1.79 85.9 0.152 6.2 3 3899
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1Y7L 1.7 22.08 29196 29196 1543 97.26 0.1737 0.1737 0.17209 0.169 0.20439 0.2024 RANDOM 15.447
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] -0.35 -0.35 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.242 r_dihedral_angle_4_deg 16.391 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 5.362 r_scangle_it 3.129 r_scbond_it 1.933 r_angle_refined_deg 1.282 r_mcangle_it 1.149 r_mcbond_it 0.754 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.242 r_dihedral_angle_4_deg 16.391 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 5.362 r_scangle_it 3.129 r_scbond_it 1.933 r_angle_refined_deg 1.282 r_mcangle_it 1.149 r_mcbond_it 0.754 r_nbtor_refined 0.302 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2366 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing