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Hydrolase StnA mutant - S185A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 0.1 M Ammonium Citrate dibasic, 0.1 M Sodium citrate pH 5.0, 20% 2-propanol, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.256 α = 115.06 b = 92.847 β = 106.09 c = 104.037 γ = 97.69
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2015-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9818 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 50 95.8 6.12 3.2 57747
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 2.9 3 96.6 0.487 2.54 3.2
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 5HDF 2.9 46.072 52120 2792 95.09 0.24637 0.24366 0.2447 0.2976 0.2961 RANDOM 51.566
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] 0.9 -1.33 1.35 0.45 -1.01 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_3_deg 13.994 r_long_range_B_refined 6.938 r_long_range_B_other 6.938 r_dihedral_angle_1_deg 6.471 r_scangle_other 4.37 r_mcangle_it 4.159 r_mcangle_other 4.159 r_scbond_it 2.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_3_deg 13.994 r_long_range_B_refined 6.938 r_long_range_B_other 6.938 r_dihedral_angle_1_deg 6.471 r_scangle_other 4.37 r_mcangle_it 4.159 r_mcangle_other 4.159 r_scbond_it 2.648 r_scbond_other 2.647 r_mcbond_it 2.54 r_mcbond_other 2.54 r_angle_refined_deg 1.37 r_angle_other_deg 0.969 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 16720 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing