☰ Navigation Tabs
Crystal structure of O-acetylhomoserine sulfhydrolase from Brucella melitensis at 2.0 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM di-ammonium tartrate pH 7.0, 12% PEG3350, 4 mM n-decyl-b-D-maltopyranoside
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.71 α = 90 b = 109.71 β = 90 c = 110.77 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 6M 2012-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 95.01 99.9 0.104 0.107 0.025 0.999 19.6 18.3 52389
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 2 2.05 99.5 1.164 16
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NMY 2 95.01 49750 2599 99.85 0.17246 0.16965 0.1773 0.22346 0.2274 RANDOM 41.576
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] 12.67 12.67 -25.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 19.827 r_dihedral_angle_3_deg 16.278 r_long_range_B_other 7.678 r_long_range_B_refined 7.677 r_dihedral_angle_1_deg 6.825 r_scangle_other 6.334 r_mcangle_it 4.84 r_mcangle_other 4.839 r_scbond_it 4.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 19.827 r_dihedral_angle_3_deg 16.278 r_long_range_B_other 7.678 r_long_range_B_refined 7.677 r_dihedral_angle_1_deg 6.825 r_scangle_other 6.334 r_mcangle_it 4.84 r_mcangle_other 4.839 r_scbond_it 4.587 r_scbond_other 4.584 r_mcbond_it 3.875 r_mcbond_other 3.875 r_angle_refined_deg 1.951 r_angle_other_deg 1.503 r_chiral_restr 0.145 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5617 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction BALBES phasing