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K98A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 2.5 M sodium chloride, 0.1 M acetate buffer, 0.2 M lithium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.53 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.901 α = 90 b = 99.901 β = 90 c = 100.589 γ = 120
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 SBC-3 2005-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 1.92 32.8 100 0.182 5.8 8.7 14934 14934 33.4
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 1.92 1.98 99.9 0.633 2.51 5.7 1215
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 3N55 1.92 32.8 14872 14872 752 99.55 0.1696 0.1696 0.1682 0.1827 0.1958 0.2136 RANDOM 29.239
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] -0.2 -0.1 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.198 r_dihedral_angle_4_deg 19.502 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.665 r_scbond_it 2.282 r_mcangle_it 1.532 r_angle_refined_deg 1.528 r_mcbond_it 0.902 r_angle_other_deg 0.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.198 r_dihedral_angle_4_deg 19.502 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.665 r_scbond_it 2.282 r_mcangle_it 1.532 r_angle_refined_deg 1.528 r_mcbond_it 0.902 r_angle_other_deg 0.851 r_mcbond_other 0.246 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 894 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling