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Crystal structure of the NUDIX domain of NUDT6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCD PDB entry 1VCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG 3350, 0.4M tri-ammonium citrate, 5mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.53 α = 90 b = 54.53 β = 90 c = 133.71 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r TIROIDAL MIRROR 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979300 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 50 99.9 0.059 0.056 22.2 10.3 23317 23294 -3 24.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.79 99.8 0.574 0.545 4.1 10.3 3305
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1VCD 1.7 19.08 21832 21832 1149 100 0.19576 0.19576 0.1944 0.198 0.22135 0.2247 RANDOM 24.756
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_1_deg 6.842 r_angle_other_deg 5.516 r_scangle_it 4.909 r_scbond_it 2.932 r_mcangle_it 2.059 r_angle_refined_deg 1.836 r_mcbond_it 1.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_1_deg 6.842 r_angle_other_deg 5.516 r_scangle_it 4.909 r_scbond_it 2.932 r_mcangle_it 2.059 r_angle_refined_deg 1.836 r_mcbond_it 1.152 r_mcbond_other 0.278 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_bond_other_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1319 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 25
Software Software Software Name Purpose ADSC data collection MrBUMP phasing REFMAC refinement XDS data reduction SCALA data scaling