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Crystal structure of Tm1382, a putative Nudix hydrolase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Trisodium Citrate pH 5.5, PEG 3000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.589 α = 90 b = 62.879 β = 98.37 c = 73.896 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 CCD MARMOSAIC 225 mm CCD 2008-04-01 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2008-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97933 APS 22-BM 2 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
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 1.89 50 99.9 0.059 3.7 34267
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 1.9 1.97 100 0.387 3.7 3396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.89 40 34212 1714 99.23 0.201 0.199 0.2054 0.24 0.2519 RANDOM 32.51
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] -0.68 -0.17 -0.15 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.955 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_4_deg 13.211 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.863 r_scbond_it 2.08 r_mcangle_it 1.342 r_mcbond_it 1.247 r_angle_refined_deg 1.216 r_angle_other_deg 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.955 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_4_deg 13.211 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.863 r_scbond_it 2.08 r_mcangle_it 1.342 r_mcbond_it 1.247 r_angle_refined_deg 1.216 r_angle_other_deg 0.798 r_symmetry_hbond_refined 0.235 r_symmetry_vdw_other 0.192 r_nbd_other 0.188 r_nbd_refined 0.187 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.169 r_mcbond_other 0.163 r_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2972 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling