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Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium chloride and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.721 α = 90 b = 64.721 β = 90 c = 77.751 γ = 120
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 PILATUS 6M-F 2018-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
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 2.7 45.5 99.5 0.096 0.996 11.4 4.3 9929
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 2.7 2.87 0.602 1.65
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 3COU 2.7 45.47 9480 448 99.52 0.1619 0.1587 0.1735 0.2313 0.2456 RANDOM 56.583
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] 2.01 2.01 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.839 r_dihedral_angle_3_deg 18.355 r_dihedral_angle_4_deg 15.161 r_dihedral_angle_1_deg 7.727 r_angle_refined_deg 1.498 r_angle_other_deg 1.151 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.839 r_dihedral_angle_3_deg 18.355 r_dihedral_angle_4_deg 15.161 r_dihedral_angle_1_deg 7.727 r_angle_refined_deg 1.498 r_angle_other_deg 1.151 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2524 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 80
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing