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Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei
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, SITTING DROP 7 289 BupsA.00264.a.A1 PS01261 at 27 mg/mL against 0.2 M NaK Tartrate, 30% PEG 3350 PACT E9 focus screen with 20% ethylene glycol as cro-protectant, crystal tracking ID 230892e11, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.04 α = 90 b = 78.04 β = 90 c = 113.92 γ = 90
Symmetry Space Group P 43 21 2
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 QUANTUM 315r 2012-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
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 2.5 50 99.3 0.06 24.52 6 12763 12669 -3 51.427
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 2.5 2.57 99.7 0.576 4.08
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 2.5 50 12668 633 99.26 0.2099 0.2077 0.2087 0.2507 0.2126 RANDOM 45.9818
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] 1.99 1.99 -3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_4_deg 19.939 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 5.961 r_angle_refined_deg 1.421 r_angle_other_deg 1.134 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_4_deg 19.939 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 5.961 r_angle_refined_deg 1.421 r_angle_other_deg 1.134 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1949 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction