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Structure of KDNase from Aspergillus Terrerus 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 6K, 0.1M MES pH6 , 0.2M Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.652 α = 90 b = 67.045 β = 90 c = 93.507 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 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9159 Diamond I04
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 1.69 67.04 98.4 0.99 8.3 5.2 43029
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 1.69 1.74 0.78
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 1.69 67.04 40778 2213 98.09 0.2023 0.2003 0.2091 0.2379 0.2455 RANDOM 25.455
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] 0.21 -0.71 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.681 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.855 r_angle_refined_deg 1.53 r_angle_other_deg 0.829 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.681 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.855 r_angle_refined_deg 1.53 r_angle_other_deg 0.829 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2943 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing