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Crystal structure of a putative enzyme (possible Nudix hydrolase) from Escherichia Coli K12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 1.8M Ammonium Sulphate, 0.1M Na Acetate pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.56 65.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.701 α = 90 b = 134.884 β = 90 c = 145.246 γ = 90
Symmetry Space Group I 2 2 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 4 mirrors 2005-08-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795, 0.97943, 0.97956 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 50 97.6 0.064 33 8.6 60149 58739 2 2
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 2.07 82.4 0.6 2.3 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 50 58739 55765 2974 98.34 0.201 0.201 0.19908 0.1979 0.23053 0.2261 RANDOM 40.936
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] 3.22 -1.1 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.056 r_dihedral_angle_4_deg 18.29 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_1_deg 6.458 r_scangle_it 3.885 r_scbond_it 2.56 r_mcangle_it 1.8 r_angle_refined_deg 1.519 r_mcbond_it 1.221 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.056 r_dihedral_angle_4_deg 18.29 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_1_deg 6.458 r_scangle_it 3.885 r_scbond_it 2.56 r_mcangle_it 1.8 r_angle_refined_deg 1.519 r_mcbond_it 1.221 r_nbtor_refined 0.3 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.165 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3882 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling SOLVE phasing RESOLVE phasing