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Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VSB 1VSB and 1CHO experimental model PDB 1CHO 1VSB and 1CHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 298 10% ethylene glycol, 480 mM sodium malate, 75 mM sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.256 α = 90 b = 100.971 β = 90 c = 115.785 γ = 90
Symmetry Space Group C 2 2 21
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 4 Mirrors 2003-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.00 ALS 5.0.3
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 1.55 74.54 95.4 0.102 0.266 14.7 6.4 88530 88530 1.5 3
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) 1.55 1.61 77.3 0.422 3.21 5.1 7071
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 1VSB and 1CHO 1.55 74.54 88530 84093 4428 85.69 0.19199 0.19199 0.19129 0.2038 0.20518 0.219 RANDOM 12.112
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] 0.47 -0.78 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.587 r_scangle_it 3.189 r_scbond_it 1.929 r_angle_refined_deg 1.598 r_angle_other_deg 1.152 r_mcangle_it 1.061 r_mcbond_it 0.551 r_symmetry_hbond_refined 0.205 r_nbd_other 0.202 r_nbd_refined 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.587 r_scangle_it 3.189 r_scbond_it 1.929 r_angle_refined_deg 1.598 r_angle_other_deg 1.152 r_mcangle_it 1.061 r_mcbond_it 0.551 r_symmetry_hbond_refined 0.205 r_nbd_other 0.202 r_nbd_refined 0.187 r_symmetry_vdw_other 0.18 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.117 r_chiral_restr 0.101 r_metal_ion_refined 0.087 r_nbtor_other 0.083 r_bond_refined_d 0.016 r_bond_other_d 0.011 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4607 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing