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Crystal structure of a putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Methanocaldococcus jannaschii DSM 2661
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 289 0.1 M Acetate,
0.8 M NaH2PO4/1.2 K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.305 α = 90 b = 119.305 β = 90 c = 170.105 γ = 120
Symmetry Space Group P 31 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 315r mirrors 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 2.65 40 99.8 0.078 35 7.1 41130 41047 2 2 75
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 2.65 2.7 100 0.7 3 7.3 2003
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.65 40 2 2 40990 38929 2061 99.36 0.205 0.20515 0.20219 0.212 0.26175 0.2662 RANDOM 30.138
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] 2.66 1.33 2.66 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.744 r_dihedral_angle_3_deg 19.799 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_1_deg 6.749 r_scangle_it 3.337 r_scbond_it 2.021 r_angle_refined_deg 1.645 r_mcangle_it 1.361 r_angle_other_deg 0.973 r_mcbond_it 0.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.744 r_dihedral_angle_3_deg 19.799 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_1_deg 6.749 r_scangle_it 3.337 r_scbond_it 2.021 r_angle_refined_deg 1.645 r_mcangle_it 1.361 r_angle_other_deg 0.973 r_mcbond_it 0.724 r_mcbond_other 0.127 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7612 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 35
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing DM model building SHELX model building MLPHARE phasing Coot model building RESOLVE model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing SHELX phasing RESOLVE phasing