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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 2XCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% Peg 3350, 0.2m K formate
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.45 α = 90 b = 74.01 β = 90 c = 160.69 γ = 90
Symmetry Space Group P 21 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 2019-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91188 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.99 47.73 98.5 0.999 8.9 5.4 405311
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.01 89.6 0.689 0.7 1
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 2xcy 0.99 47.73 385221 19946 98.49 0.2192 0.218 0.2222 0.2407 0.244 RANDOM 12.478
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] 0.27 -0.69 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_sphericity_free 24.228 r_dihedral_angle_4_deg 17.441 r_sphericity_bonded 15.034 r_dihedral_angle_3_deg 11.097 r_dihedral_angle_1_deg 7.164 r_rigid_bond_restr 5.798 r_angle_refined_deg 1.614 r_angle_other_deg 0.85 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_sphericity_free 24.228 r_dihedral_angle_4_deg 17.441 r_sphericity_bonded 15.034 r_dihedral_angle_3_deg 11.097 r_dihedral_angle_1_deg 7.164 r_rigid_bond_restr 5.798 r_angle_refined_deg 1.614 r_angle_other_deg 0.85 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5857 Nucleic Acid Atoms Solvent Atoms 900 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing