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Thermolysin by LB nanotemplate method after high X-Ray dose on ESRF ID14-2 beamline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DNZ PDB ENTRY 3DNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.562 α = 90 b = 92.562 β = 90 c = 128.712 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 Toroidal mirror 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.194 80.161 84 0.238 0.238 2.9 5.4 89247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.18 1.25 30.8 1.3 4653
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DNZ 1.22 68.04 57583 2911 59.4 0.239 0.238 0.261 0.2347 RANDOM 16.835
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] -0.75 -0.38 -0.75 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.368 r_dihedral_angle_4_deg 17.439 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.087 r_scangle_it 1.5 r_mcangle_it 1.295 r_angle_refined_deg 1.073 r_scbond_it 1.013 r_mcbond_it 0.817 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.368 r_dihedral_angle_4_deg 17.439 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.087 r_scangle_it 1.5 r_mcangle_it 1.295 r_angle_refined_deg 1.073 r_scbond_it 1.013 r_mcbond_it 0.817 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.088 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2479 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 22
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing