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The leupeptin-trypsin covalent complex at 1.14 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGE PDB entry 2AGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.81 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.888 α = 90 b = 63.562 β = 90 c = 69.102 γ = 90
Symmetry Space Group P 21 21 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 2003-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.00000 ALS 8.3.1
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 1.14 46.63 99.64 0.04 0.04 13.1 3.2 88464 88464 -3
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) 1 1.14 1.2 0.284 0.284 1.5 1.3 6920
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 PDB entry 2AGE 1.14 46.63 88464 88464 4449 99.64 0.117 0.117 0.116 0.1176 0.138 0.1404 inherited from PDB entry 2AGE 12.663
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] -0.06 -0.09 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.098 r_sphericity_free 16.976 r_dihedral_angle_4_deg 11.996 r_dihedral_angle_3_deg 10.309 r_sphericity_bonded 6.875 r_scangle_it 6.73 r_dihedral_angle_1_deg 6.677 r_scbond_it 5.283 r_mcangle_it 3.977 r_rigid_bond_restr 3.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.098 r_sphericity_free 16.976 r_dihedral_angle_4_deg 11.996 r_dihedral_angle_3_deg 10.309 r_sphericity_bonded 6.875 r_scangle_it 6.73 r_dihedral_angle_1_deg 6.677 r_scbond_it 5.283 r_mcangle_it 3.977 r_rigid_bond_restr 3.471 r_mcbond_it 3.083 r_mcbond_other 2.198 r_angle_other_deg 1.904 r_angle_refined_deg 1.869 r_nbd_refined 0.377 r_symmetry_vdw_other 0.356 r_nbd_other 0.27 r_symmetry_hbond_refined 0.229 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.137 r_metal_ion_refined 0.121 r_nbtor_other 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1654 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 11
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling TRUNCATE data reduction EPMR phasing REFMAC refinement CCP4 data scaling TRUNCATE data scaling