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Structure of Mycobacterium tuberculosis CYP121 in complex with the antifungal drug fluconazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N40 1N40/2IJ5 experimental model PDB 2IJ5 1N40/2IJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 PEG 3350 and 0.2M NaSCN, saturating fluconazole conc., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.805 α = 90 b = 129.898 β = 90 c = 323.393 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 CCD ADSC QUANTUM 210 2005-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.93 ESRF ID14-3
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 1.9 20 98.9 0.087 9.4 166629 166629
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 1N40/2IJ5 1.9 20 166629 166629 8786 89.9 0.17035 0.17035 0.16736 0.1762 0.22644 0.2336 RANDOM 26.878
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] 0.34 0.42 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.76 r_dihedral_angle_4_deg 16.31 r_dihedral_angle_3_deg 14.844 r_sphericity_free 5.899 r_dihedral_angle_1_deg 5.647 r_scangle_it 3.394 r_scbond_it 2.452 r_angle_refined_deg 1.601 r_mcangle_it 1.548 r_sphericity_bonded 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.76 r_dihedral_angle_4_deg 16.31 r_dihedral_angle_3_deg 14.844 r_sphericity_free 5.899 r_dihedral_angle_1_deg 5.647 r_scangle_it 3.394 r_scbond_it 2.452 r_angle_refined_deg 1.601 r_mcangle_it 1.548 r_sphericity_bonded 1.462 r_rigid_bond_restr 1.349 r_mcbond_it 1.25 r_angle_other_deg 0.867 r_mcbond_other 0.408 r_symmetry_vdw_other 0.288 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.215 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.134 r_chiral_restr 0.091 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_xyhbond_nbd_other 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18072 Nucleic Acid Atoms Solvent Atoms 1982 Heterogen Atoms 434
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing