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proteinase K- digalacturonic acid complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PRK PDB ENTRY 3PRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 5% PEG 3350, 0.1 M HEPES; reservoir of 25% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.72 α = 90 b = 67.72 β = 90 c = 101.89 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 100 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.32 32.14 94 0.066 11.5 5.33 53100 53026 15.9
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 1.32 1.37 46.2 0.482 1.3 1.5 2566
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 3PRK 1.32 30.36 49454 49454 2646 92.33 0.16036 0.16036 0.1579 0.1625 0.20669 0.2115 RANDOM 15.875
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] -0.45 -0.45 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 19.321 r_dihedral_angle_3_deg 12.819 r_sphericity_free 8.481 r_dihedral_angle_1_deg 6.234 r_scangle_it 5.315 r_sphericity_bonded 4.871 r_scbond_it 4.085 r_mcangle_it 3.353 r_mcbond_it 2.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 19.321 r_dihedral_angle_3_deg 12.819 r_sphericity_free 8.481 r_dihedral_angle_1_deg 6.234 r_scangle_it 5.315 r_sphericity_bonded 4.871 r_scbond_it 4.085 r_mcangle_it 3.353 r_mcbond_it 2.568 r_rigid_bond_restr 2.377 r_mcbond_other 2.262 r_angle_refined_deg 1.265 r_angle_other_deg 0.674 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling