☰ Navigation Tabs
Proteinase K by LB nanotemplate method after the third 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 3DE0 PDB ENTRY 3DE0
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 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.669 α = 90 b = 67.669 β = 90 c = 101.625 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 2007-02-07 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 2 56.344 90.4 0.128 0.128 4.6 5.1 14864
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) 2 2.11 90.7 0.258 0.258 2.1 5.2 2130
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 3DE0 2 34.84 14826 734 89.48 0.182 0.181 0.1821 0.206 0.2088 RANDOM 5.64
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 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 21.391 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.036 r_scangle_it 1.978 r_mcangle_it 1.56 r_scbond_it 1.465 r_angle_refined_deg 1.38 r_metal_ion_refined 1.379 r_mcbond_it 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 21.391 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.036 r_scangle_it 1.978 r_mcangle_it 1.56 r_scbond_it 1.465 r_angle_refined_deg 1.38 r_metal_ion_refined 1.379 r_mcbond_it 1.008 r_symmetry_hbond_refined 0.513 r_symmetry_vdw_refined 0.443 r_nbtor_refined 0.316 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
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