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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 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.936 α = 98 b = 45.655 β = 115.13 c = 47.248 γ = 113.41
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 2009-07-07 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 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 2.1 24.108 93.6 0.092 3.8 15131 15131
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) 2.1 2.21 0.56 2.5 3.8 2152
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 2.1 24.108 15129 769 93.65 0.185 0.182 0.1878 0.237 0.2381 RANDOM 30.249
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] -0.02 0.17 0.03 0.1 0.19 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.664 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.399 r_dihedral_angle_1_deg 6.301 r_scangle_it 2.291 r_scbond_it 1.444 r_angle_refined_deg 1.229 r_mcangle_it 0.918 r_mcbond_it 0.515 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.664 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.399 r_dihedral_angle_1_deg 6.301 r_scangle_it 2.291 r_scbond_it 1.444 r_angle_refined_deg 1.229 r_mcangle_it 0.918 r_mcbond_it 0.515 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2468 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 3
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction