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Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)
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 2.36 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.045 α = 64.39 b = 78.364 β = 64.69 c = 88.843 γ = 65.03
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 MARRESEACH MIRRORS 2005-05-20 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 2.65 15 89.1 0.15 4.4 2.5 59532 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 2.65 2.71 85.7 0.48 1.25 1.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W19 2.75 10 35562 1897 89.5 0.254 0.25 0.2535 0.324 RANDOM 32.84
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] 0.74 -1.17 -0.08 -0.1 1.23 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_1_deg 4.16 r_angle_refined_deg 1.168 r_nbtor_refined 0.285 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_1_deg 4.16 r_angle_refined_deg 1.168 r_nbtor_refined 0.285 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.125 r_scangle_it 0.066 r_chiral_restr 0.063 r_scbond_it 0.048 r_mcangle_it 0.021 r_mcbond_it 0.01 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 10598 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 291
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing