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Proteinase K by Classical hanging drop method after high X-Ray dose on ESRF ID14-2 beamline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PTK PDB ENTRY 1PTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20mg/ml of protein in 25mM HEPES pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microlitres of protein solution with 4 microlitres of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.948 α = 90 b = 67.948 β = 90 c = 102.388 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 110 CCD ADSC QUANTUM 4 Toroidal mirror 2007-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 1.2 ESRF ID14-2
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 0.99 56.615 86.1 0.09 0.09 5.6 5.8 114171
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) 0.99 1.05 35 0.768 0.768 0.9 1.5 6600
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 1PTK 0.99 48.06 113883 5724 86.12 0.221 0.221 0.2207 0.222 0.222 RANDOM 7.099
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.577 r_dihedral_angle_4_deg 13.98 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 5.501 r_scangle_it 1.399 r_angle_refined_deg 1.087 r_mcangle_it 1.049 r_scbond_it 1.034 r_mcbond_it 0.607 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.577 r_dihedral_angle_4_deg 13.98 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 5.501 r_scangle_it 1.399 r_angle_refined_deg 1.087 r_mcangle_it 1.049 r_scbond_it 1.034 r_mcbond_it 0.607 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.308 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.127 r_metal_ion_refined 0.106 r_chiral_restr 0.076 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2021 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction