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Crystal Structure of S302G single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.2 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y7L 1Y7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 1.3 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.6 α = 90 b = 112.6 β = 90 c = 45.73 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 IMAGE PLATE MAR scanner 345 mm plate 2014-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.271 42.37 96.02 0.788 44.88 14.4 12952
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.271 2.352 0.745
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Y7L 2.271 42.37 12916 625 96.023 0.225 0.2225 0.2235 0.2664 0.2693 32.709
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] -2.295 -2.295 4.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_4_deg 21.385 r_dihedral_angle_3_deg 17.441 r_dihedral_angle_1_deg 7.026 r_lrange_it 5.939 r_scangle_it 3.701 r_mcangle_it 3.392 r_scbond_it 2.536 r_mcbond_it 2.2 r_angle_refined_deg 1.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_4_deg 21.385 r_dihedral_angle_3_deg 17.441 r_dihedral_angle_1_deg 7.026 r_lrange_it 5.939 r_scangle_it 3.701 r_mcangle_it 3.392 r_scbond_it 2.536 r_mcbond_it 2.2 r_angle_refined_deg 1.565 r_nbtor_refined 0.301 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.19 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.119 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing