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Crystal structure of the complex of proteinase K with auramine at 1.8A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 NaNO3 , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.299 α = 90 b = 68.299 β = 90 c = 108.379 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 IMAGE PLATE MAR scanner 345 mm plate Mirror 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 57.74 95.2 24890 22500
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.79 1.83 99
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1IC6 1.79 57.74 24890 22500 1198 95.22 0.15822 0.15576 0.20493 RANDOM 16.276
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] 0.12 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.964 r_dihedral_angle_4_deg 19.982 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.47 r_scbond_it 2.15 r_angle_refined_deg 1.243 r_mcangle_it 1.139 r_mcbond_it 0.742 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.964 r_dihedral_angle_4_deg 19.982 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.47 r_scbond_it 2.15 r_angle_refined_deg 1.243 r_mcangle_it 1.139 r_mcbond_it 0.742 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_refined 0.129 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.09 r_metal_ion_refined 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2073 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing