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Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNYDI
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 2.1 41.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.153 α = 90 b = 112.153 β = 90 c = 45.728 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++ 2009-01-12 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 26.44 89 0.056 21.6 4 20150 20150
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 69.5 0.23 6.3 3.9 2272
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 26.44 19121 19121 1003 88.98 0.16503 0.16503 0.16271 0.1618 0.20869 0.2075 RANDOM 18.195
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] -0.83 -0.83 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.499 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_3_deg 14.574 r_dihedral_angle_1_deg 5.853 r_scangle_it 3.277 r_scbond_it 2.103 r_angle_refined_deg 1.39 r_mcangle_it 1.273 r_mcbond_it 0.84 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.499 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_3_deg 14.574 r_dihedral_angle_1_deg 5.853 r_scangle_it 3.277 r_scbond_it 2.103 r_angle_refined_deg 1.39 r_mcangle_it 1.273 r_mcbond_it 0.84 r_nbtor_refined 0.297 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.097 r_bond_refined_d 0.014 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 2364 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 5
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing