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Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 19% PEG 3350, 600mM ammonium chloride, pH 7.0, Vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.95 α = 73.47 b = 43.877 β = 74.06 c = 55.967 γ = 62.66
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 MAR CCD 165 mm 2008-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 52.882 97.2 0.081 0.081 8.4 3.9 35983 34975 25.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 95.8 0.511 0.511 2 3.9 5017
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.7 20 35950 34958 1752 97.24 0.223 0.221 0.2285 0.264 0.2685 RANDOM 35.158
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] 0.09 -0.93 1.35 1.21 -0.49 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 17.319 r_dihedral_angle_1_deg 6.081 r_scangle_it 4.717 r_scbond_it 2.86 r_mcangle_it 1.685 r_angle_refined_deg 1.59 r_mcbond_it 0.948 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 17.319 r_dihedral_angle_1_deg 6.081 r_scangle_it 4.717 r_scbond_it 2.86 r_mcangle_it 1.685 r_angle_refined_deg 1.59 r_mcbond_it 0.948 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building