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Crystal structure of a subtilisin-like protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LPC PDB ENTRY 3LPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Sodium Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.059 α = 97.79 b = 45.98 β = 115.24 c = 47.243 γ = 113.86
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-08-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.542
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 2 39.659 93.9 0.06 0.06 13.5 2.3 17666 17666
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 89.3 0.265 0.265 2.7 2.3 2459
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 PDB ENTRY 3LPC 2 24.26 17664 915 93.98 0.18 0.177 0.1864 0.233 0.241 RANDOM 24.903
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] 0.07 -0.01 -0.02 -0.11 -0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.145 r_dihedral_angle_4_deg 19.354 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 6.163 r_scangle_it 1.622 r_mcangle_it 1.488 r_angle_refined_deg 1.343 r_scbond_it 1.091 r_mcbond_it 0.947 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.145 r_dihedral_angle_4_deg 19.354 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 6.163 r_scangle_it 1.622 r_mcangle_it 1.488 r_angle_refined_deg 1.343 r_scbond_it 1.091 r_mcbond_it 0.947 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2495 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 3
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection