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Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COU PDB ENTRY 3COU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS MIXED WITH 5MM MGCL2 AND 2MM IDP PRIOR SETTING-UP THE PLATES. THEN IT WAS CRYSTALLIZED FROM 20MM MGCL2, 22% W/V POLYACRYLIC ACID 5100 AND 0.1M HEPES PH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.583 α = 90 b = 141.583 β = 90 c = 141.583 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 ADSC CCD MIRRORS 2010-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.72 42.69 100 0.06 11.3 6.8 25010 -3 21.062
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 1.72 1.81 100 0.7 1.1 6.6
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 PDB ENTRY 3COU 1.72 81.74 23737 1273 99.97 0.15983 0.15864 0.1654 0.18145 0.1866 RANDOM 15.756
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.129 r_dihedral_angle_4_deg 14.596 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_1_deg 5.553 r_scangle_it 3.322 r_scbond_it 1.946 r_angle_refined_deg 1.276 r_mcangle_it 1.269 r_angle_other_deg 0.838 r_mcbond_it 0.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.129 r_dihedral_angle_4_deg 14.596 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_1_deg 5.553 r_scangle_it 3.322 r_scbond_it 1.946 r_angle_refined_deg 1.276 r_mcangle_it 1.269 r_angle_other_deg 0.838 r_mcbond_it 0.666 r_mcbond_other 0.133 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1393 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing