☰ Navigation Tabs
Proteinase K by LB nanotemplate method after the first step of high X-Ray dose on ESRF ID23-1 beamline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D9Q PDB entry 3D9Q
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 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.693 α = 90 b = 67.693 β = 90 c = 101.658 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 CCD ADSC QUANTUM 315 mirror 2007-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 1.7 40 87.6 0.122 0.122 4.7 4.6 23245
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) 1.7 1.79 76.8 0.335 0.335 1.5 3.3 2909
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3D9Q 1.7 34.85 23198 1166 86.91 0.198 0.196 0.226 0.2485 RANDOM 6.471
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] -0.18 -0.18 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 5.728 r_scangle_it 1.882 r_mcangle_it 1.397 r_scbond_it 1.359 r_angle_refined_deg 1.214 r_mcbond_it 0.874 r_symmetry_hbond_refined 0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 5.728 r_scangle_it 1.882 r_mcangle_it 1.397 r_scbond_it 1.359 r_angle_refined_deg 1.214 r_mcbond_it 0.874 r_symmetry_hbond_refined 0.518 r_symmetry_vdw_refined 0.426 r_nbtor_refined 0.316 r_metal_ion_refined 0.263 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
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 ADSC data collection