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A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.335 α = 90 b = 89.215 β = 90 c = 160.873 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2001-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 1.0 EMBL/DESY, HAMBURG X11
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 1.05 20 95.8 0.071 0.071 5.1 2.6 440216 440216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 93.9 0.485 1.6 1.9 62782
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1E1L 1.05 40 440131 440131 2200 95.41 0.1339 0.13393 0.13393 0.1362 0.153 RANDOM 12.815
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] 0.17 -0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.938 r_sphericity_free 10.895 r_dihedral_angle_1_deg 5.086 r_sphericity_bonded 4.947 r_scangle_it 4.498 r_scbond_it 3 r_mcangle_it 2.172 r_angle_refined_deg 1.747 r_mcbond_it 1.468 r_rigid_bond_restr 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.938 r_sphericity_free 10.895 r_dihedral_angle_1_deg 5.086 r_sphericity_bonded 4.947 r_scangle_it 4.498 r_scbond_it 3 r_mcangle_it 2.172 r_angle_refined_deg 1.747 r_mcbond_it 1.468 r_rigid_bond_restr 1.382 r_nbtor_other 0.987 r_angle_other_deg 0.918 r_symmetry_vdw_refined 0.426 r_nbd_refined 0.395 r_xyhbond_nbd_other 0.307 r_symmetry_hbond_refined 0.302 r_xyhbond_nbd_refined 0.241 r_symmetry_vdw_other 0.239 r_nbd_other 0.213 r_chiral_restr 0.157 r_symmetry_hbond_other 0.094 r_bond_refined_d 0.015 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6908 Nucleic Acid Atoms Solvent Atoms 1864 Heterogen Atoms 248
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling BEAST model building REFMAC refinement CCP4 data scaling BEAST phasing