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Proteinase K by LB nanotemplate method after the second 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 3DDZ PDB ENTRY 3DDZ
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 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.664 α = 90 b = 67.664 β = 90 c = 101.622 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 2007-07-02 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 1.9 56.344 89.9 0.131 0.131 4.4 5 17199
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) 1.9 2 89.3 0.293 0.293 1.8 5.2 2460
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 3DDZ 1.9 34.83 17158 878 89.06 0.19 0.188 0.23 0.2457 RANDOM 5.88
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.395 r_dihedral_angle_4_deg 22.469 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 5.987 r_scangle_it 1.989 r_mcangle_it 1.531 r_scbond_it 1.471 r_angle_refined_deg 1.305 r_metal_ion_refined 1.094 r_mcbond_it 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.395 r_dihedral_angle_4_deg 22.469 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 5.987 r_scangle_it 1.989 r_mcangle_it 1.531 r_scbond_it 1.471 r_angle_refined_deg 1.305 r_metal_ion_refined 1.094 r_mcbond_it 0.997 r_symmetry_hbond_refined 0.505 r_symmetry_vdw_refined 0.434 r_nbtor_refined 0.317 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.083 r_bond_refined_d 0.012 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 REFMAC phasing