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Crystal structure of human Nudix motif 16 (NUDT16)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U20 PDB entry 1U20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 0.1M CHES pH 9.5, 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.13 α = 90 b = 142.13 β = 90 c = 142.13 γ = 90
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 MARMOSAIC 225 mm CCD Mirrors 2008-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9795 BESSY 14.1
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 1.8 20 99.9 0.067 0.067 8.9 5.8 22101
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) 1.8 1.9 100 0.574 0.574 1.3 3.8 3212
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 1U20 1.8 19.71 21790 21790 1117 98.57 0.186 0.186 0.184 0.1886 0.217 0.224 RANDOM 13.855
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 r_dihedral_angle_2_deg 30.476 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_4_deg 13.107 r_dihedral_angle_1_deg 6.28 r_angle_other_deg 4.291 r_scangle_it 4.154 r_scbond_it 2.765 r_mcangle_it 1.638 r_angle_refined_deg 1.62 r_mcbond_it 0.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.476 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_4_deg 13.107 r_dihedral_angle_1_deg 6.28 r_angle_other_deg 4.291 r_scangle_it 4.154 r_scbond_it 2.765 r_mcangle_it 1.638 r_angle_refined_deg 1.62 r_mcbond_it 0.969 r_symmetry_vdw_other 0.304 r_nbd_other 0.258 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.177 r_nbtor_refined 0.173 r_nbtor_other 0.109 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1436 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction