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Crystal structure of a Nudix Hydrolase from M. Smegmatis, RenU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1-1.4 M NaAc, 0.1 M BTP pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.198 α = 90 b = 118.738 β = 92.32 c = 36.432 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 PILATUS3 S 6M 2016-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.93927 ALS 5.0.2
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 2.1 59.37 93.6 0.072 0.087 0.047 9 3.2 15812
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 2.1 2.14 72.3 0.177 0.218 0.124 0.961 2.6
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 3HHJ 2.1 59.37 15093 683 93.05 0.1828 0.1804 0.1918 0.2311 0.2439 RANDOM 43.721
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] 7.53 1.04 -3.51 -4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_4_deg 13.743 r_dihedral_angle_1_deg 7.089 r_angle_refined_deg 1.601 r_angle_other_deg 0.963 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_4_deg 13.743 r_dihedral_angle_1_deg 7.089 r_angle_refined_deg 1.601 r_angle_other_deg 0.963 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2372 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction