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Human NUDT1 with medetomidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NUDT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30% PEG8000, 0.2 M lithium sulfate and 0.1 M acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.739 α = 90 b = 60.85 β = 90 c = 67.53 γ = 90
Symmetry Space Group P 2 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 PILATUS 2M 2015-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928190 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.3 67.53 99.9 0.061 13.4 6.5 38033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 99.9 0.693 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 45.205 37960 1935 99.868 0.161 0.1592 0.1674 0.2065 0.2061 16.151
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] 0.413 -0.492 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.714 r_dihedral_angle_4_deg 11.251 r_dihedral_angle_3_deg 10.718 r_dihedral_angle_1_deg 7.315 r_lrange_it 2.968 r_lrange_other 2.967 r_scangle_it 2.184 r_scangle_other 2.184 r_mcangle_other 1.755 r_mcangle_it 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.714 r_dihedral_angle_4_deg 11.251 r_dihedral_angle_3_deg 10.718 r_dihedral_angle_1_deg 7.315 r_lrange_it 2.968 r_lrange_other 2.967 r_scangle_it 2.184 r_scangle_other 2.184 r_mcangle_other 1.755 r_mcangle_it 1.751 r_scbond_it 1.683 r_scbond_other 1.682 r_angle_refined_deg 1.428 r_angle_other_deg 1.311 r_mcbond_it 1.254 r_mcbond_other 1.241 r_rigid_bond_restr 1.118 r_symmetry_nbd_refined 0.286 r_nbd_refined 0.202 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.163 r_nbd_other 0.144 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.072 r_gen_planes_refined 0.007 r_bond_refined_d 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 1246 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing