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Intracellular subtilisin precursor from B. clausii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJC PDB ENTRY 1YJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M BISTRIS PH 6.5, 0.1M NACL, 1.5M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.829 α = 90 b = 119.829 β = 90 c = 106.2 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 CCD 2009-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.45 46.6 100 0.18 11.6 3.6 62796 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 2.45 2.58 99.9 0.66 1.2 3.2
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 1YJC 2.45 46.62 58858 3905 100 0.202 0.197 0.1964 0.274 0.2723 RANDOM 30.49
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] 2.52 1.26 2.52 -3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 20.752 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_1_deg 6.978 r_angle_refined_deg 1.646 r_scangle_it 1.245 r_scbond_it 0.809 r_mcangle_it 0.435 r_mcbond_it 0.25 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 20.752 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_1_deg 6.978 r_angle_refined_deg 1.646 r_scangle_it 1.245 r_scbond_it 0.809 r_mcangle_it 0.435 r_mcbond_it 0.25 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13168 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 5
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing PHASER phasing REFMAC refinement