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Tetrameric structure of apo-7,8-Dihydroneopterin Aldolase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBU PDB ENTRY 1NBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 300 PEG 4000, SODIUM ACETATE, PH 4.6, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.73 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.957 α = 90 b = 72.957 β = 90 c = 42.868 γ = 90
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 4 2003-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9786 NSLS X8C
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 2.5 100 99 0.078 31.3 3990 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 2.5 3 100 0.371 7.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NBU 2.5 51.57 3548 3548 393 98.75 0.18441 0.18441 0.17854 0.1819 0.23429 0.1802 RANDOM 37.451
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] -0.93 -0.93 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.585 r_dihedral_angle_4_deg 24.087 r_dihedral_angle_3_deg 16.679 r_dihedral_angle_1_deg 8.864 r_scangle_it 5.585 r_scbond_it 3.565 r_mcangle_it 2.475 r_angle_refined_deg 2.261 r_mcbond_it 1.363 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.585 r_dihedral_angle_4_deg 24.087 r_dihedral_angle_3_deg 16.679 r_dihedral_angle_1_deg 8.864 r_scangle_it 5.585 r_scbond_it 3.565 r_mcangle_it 2.475 r_angle_refined_deg 2.261 r_mcbond_it 1.363 r_nbtor_refined 0.315 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.24 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.139 r_symmetry_hbond_refined 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 821 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement