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LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W19 PDB ENTRY 1W19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.033 α = 64.32 b = 76.692 β = 64.41 c = 86.254 γ = 63.6
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 MARRESEARCH 2007-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.3 30 97.7 0.08 6.9 2.7 62709 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 2.3 2.36 96.4 0.44 1.3 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W19 2.3 30 62709 3352 97.7 0.262 0.26 0.2592 0.299 0.2971 RANDOM 39.41
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] -1.02 -0.9 1.63 0.33 0.9 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 13.961 r_dihedral_angle_1_deg 5.02 r_angle_refined_deg 1.041 r_scangle_it 0.583 r_scbond_it 0.341 r_nbtor_refined 0.29 r_mcangle_it 0.29 r_symmetry_vdw_refined 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 13.961 r_dihedral_angle_1_deg 5.02 r_angle_refined_deg 1.041 r_scangle_it 0.583 r_scbond_it 0.341 r_nbtor_refined 0.29 r_mcangle_it 0.29 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.187 r_mcbond_it 0.157 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10701 Nucleic Acid Atoms Solvent Atoms 770 Heterogen Atoms 295
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing