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Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1mM sodium cacodylate pH 6.5, 1M sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.78 74.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.578 α = 90 b = 90.578 β = 90 c = 97.056 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 83 CCD ADSC QUANTUM 1 2014-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9798 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.77 30 98.7 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 89.4 2 3.1
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 2GTA 2.8 30 20632 1059 98.86 0.2232 0.2217 0.2216 0.2537 0.2535 RANDOM 46
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] -0.22 -0.11 -0.22 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.257 r_dihedral_angle_3_deg 20.603 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_1_deg 4.738 r_mcangle_it 1.677 r_scbond_it 1.378 r_angle_refined_deg 1.318 r_mcbond_it 0.955 r_chiral_restr 0.086 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.257 r_dihedral_angle_3_deg 20.603 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_1_deg 4.738 r_mcangle_it 1.677 r_scbond_it 1.378 r_angle_refined_deg 1.318 r_mcbond_it 0.955 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2948 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing