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Crystal structure of the F36A mutant of HsNUDT16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 293 PEG 8000, CHES
Crystal Properties Matthews coefficient Solvent content 1.95 36.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.202 α = 90 b = 49.589 β = 114.59 c = 64.284 γ = 90
Symmetry Space Group P 1 21 1
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 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 92 0.07 0.09 0.055 20.3 2.5 13719
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 74.3 0.135 0.183 0.123 0.956 1.7
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 FOURIER SYNTHESIS THROUGHOUT pdbid XX 2.3 50 13077 633 91.75 0.1919 0.1889 0.1954 0.2533 0.256 RANDOM 29.92
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] 0.29 -0.39 -0.84 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.815 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 16.916 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.612 r_angle_other_deg 0.986 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.815 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 16.916 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.612 r_angle_other_deg 0.986 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing Coot model building HKL-2000 data reduction