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Structure of KDNase from Trichophyton Rubrum in complex with 2-keto-3-deoxynononic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 25% PEG 1500, 0.1M MMT pH8
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.922 α = 90 b = 74.472 β = 90 c = 161.365 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 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) Rrim I (All) 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 0.91 80.69 84.3 0.048 0.999 14.6 5.2 226869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.91 0.93 0.821 0.534
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 2xzj 0.91 80.68 215570 11219 84.32 0.1411 0.1403 0.1435 0.1556 0.1585 RANDOM 11
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] -1.09 0.78 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_sphericity_free 23.07 r_dihedral_angle_4_deg 15.303 r_sphericity_bonded 11.401 r_dihedral_angle_3_deg 10.754 r_dihedral_angle_1_deg 7.217 r_rigid_bond_restr 4.817 r_angle_refined_deg 1.565 r_angle_other_deg 0.878 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_sphericity_free 23.07 r_dihedral_angle_4_deg 15.303 r_sphericity_bonded 11.401 r_dihedral_angle_3_deg 10.754 r_dihedral_angle_1_deg 7.217 r_rigid_bond_restr 4.817 r_angle_refined_deg 1.565 r_angle_other_deg 0.878 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing