☰ Navigation Tabs
Structure of Trichophyton Rubrum KDNase in complex with 2,3-difluoro-KDN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 25% PEG 1500, 0.1M SPG pH4
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.91 α = 90 b = 179.49 β = 103.89 c = 98.07 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M-F 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.75 95.2 96.6 0.077 0.99 8.8 2.7 158507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 94.5 0.712 1 2.3
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 2XCY 1.75 95.2 150514 7944 96.33 0.1853 0.1838 0.2133 0.2229 RANDOM 23.655
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] 0.19 -0.11 0.42 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.785 r_dihedral_angle_4_deg 15.728 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 6.853 r_angle_refined_deg 1.431 r_angle_other_deg 0.782 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.785 r_dihedral_angle_4_deg 15.728 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 6.853 r_angle_refined_deg 1.431 r_angle_other_deg 0.782 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11739 Nucleic Acid Atoms Solvent Atoms 1889 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing