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Crystal structure of NUDIX hydrolase from Nitrosomonas europaea
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 0.1 M Bis-Tris, 0.2 M Magnesium chloride, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.781 α = 90 b = 49.506 β = 106.28 c = 110.19 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2007-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 37.2 83 0.087 11.5 6.7 51323 51323 40.8
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 2.05 47.8 0.506 2.05 4.6 2106
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 37.2 51312 51312 2582 82.94 0.183 0.183 0.181 0.233 0.2699 RANDOM 35.641
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] -1.92 -0.11 3.51 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 16.585 r_dihedral_angle_1_deg 6.739 r_scangle_it 3.921 r_scbond_it 2.536 r_angle_refined_deg 1.668 r_mcangle_it 1.554 r_angle_other_deg 0.989 r_mcbond_it 0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 16.585 r_dihedral_angle_1_deg 6.739 r_scangle_it 3.921 r_scbond_it 2.536 r_angle_refined_deg 1.668 r_mcangle_it 1.554 r_angle_other_deg 0.989 r_mcbond_it 0.865 r_symmetry_vdw_other 0.286 r_mcbond_other 0.22 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.208 r_nbd_other 0.204 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.128 r_metal_ion_refined 0.113 r_chiral_restr 0.106 r_nbtor_other 0.09 r_bond_refined_d 0.018 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 5774 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 49
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing