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Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNWNI
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 10.5 298 CAPS, Ammonium Sulfate, Lithium Sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.474 α = 90 b = 112.474 β = 90 c = 45.928 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++ 2009-05-29 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 1.9 29.04 99.2 0.029 31.8 3.8 22692 22692
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) 1.9 2 95.7 0.103 8.6 2.5 3133
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 1.9 28.14 21544 21544 1127 99.17 0.16823 0.16823 0.16634 0.166 0.20534 0.2071 RANDOM 20.118
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] -0.4 -0.4 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.584 r_dihedral_angle_4_deg 19.008 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 5.621 r_scangle_it 3.492 r_scbond_it 2.229 r_angle_refined_deg 1.409 r_mcangle_it 1.322 r_mcbond_it 0.876 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.584 r_dihedral_angle_4_deg 19.008 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 5.621 r_scangle_it 3.492 r_scbond_it 2.229 r_angle_refined_deg 1.409 r_mcangle_it 1.322 r_mcbond_it 0.876 r_nbtor_refined 0.299 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2371 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing