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D37A 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 6.5 291 0.2 M calcium chloride, 0.1 M Bis-Tris buffer, 45% 2-methyl-2,4-pentanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.33 63.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.986 α = 90 b = 97.986 β = 90 c = 65.844 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 ADSC QUANTUM 315 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.94 39.3 100 0.132 8.5 5.5 51991 51991 39.1
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 1.94 1.97 100 0.718 2.12 5.1 2630
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 1.94 39.3 51985 51985 5184 99.89 0.1296 0.1296 0.127 0.1399 0.1524 0.1585 RANDOM 23.0839
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] 5.26 5.26 -10.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.003 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_4_deg 14.741 r_dihedral_angle_1_deg 7.077 r_scangle_it 2.895 r_scbond_it 1.971 r_angle_refined_deg 1.677 r_mcangle_it 1.256 r_angle_other_deg 1.096 r_mcbond_it 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.003 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_4_deg 14.741 r_dihedral_angle_1_deg 7.077 r_scangle_it 2.895 r_scbond_it 1.971 r_angle_refined_deg 1.677 r_mcangle_it 1.256 r_angle_other_deg 1.096 r_mcbond_it 0.782 r_mcbond_other 0.229 r_chiral_restr 0.127 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3644 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-3000 data scaling