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Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 6.25 % (w/v) PEG 400, 6.25 % (w/v) PEG 500 MME, 6.25 % (w/v) PEG 600, 6.25 % (w/v) PEG 1000, 0.04 M CaCl2, 0.04 M sodium formate and 0.1 M Tris-HCl at pH 8.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.105 α = 90 b = 61.744 β = 90 c = 84.325 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.6 84.32 100 0.155 0.162 0.045 0.996 9.2 13.2 40809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 2.063 2.164 0.645 0.624 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 49.82 1.33 40709 2054 99.9 0.183 0.1814 0.1815 0.2132 0.2133
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.722 f_angle_d 0.809 f_chiral_restr 0.05 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2634 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Aimless data scaling autoPROC data reduction PHASER phasing