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Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE
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 6.4 pH 6.40
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.955 α = 64.27 b = 79.959 β = 64.39 c = 88.352 γ = 62.81
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE MARRESEARCH MIRROR 2005-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ROTATING ANODE
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 2.8 20 84 0.12 4 2 77471 1
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 2.8 2.86 80.9 0.57 1.24 2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W19 2.8 12 31693 1721 82 0.262 0.259 0.326 RANDOM 31.96
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] 0.29 -2.29 1.54 0.31 0.46 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 17.114 r_dihedral_angle_3_deg 16.436 r_dihedral_angle_1_deg 4.827 r_angle_refined_deg 1.338 r_scangle_it 0.605 r_scbond_it 0.387 r_nbtor_refined 0.287 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 17.114 r_dihedral_angle_3_deg 16.436 r_dihedral_angle_1_deg 4.827 r_angle_refined_deg 1.338 r_scangle_it 0.605 r_scbond_it 0.387 r_nbtor_refined 0.287 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.16 r_mcangle_it 0.139 r_metal_ion_refined 0.103 r_chiral_restr 0.077 r_mcbond_it 0.055 r_bond_refined_d 0.009 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_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 10598 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 353
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing