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Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-4-(4-(2,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WX2 PDB ENTRY 2WX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.0, 19% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.528 α = 90 b = 128.528 β = 90 c = 116.721 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESERCH MIRRORS 2013-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.04 116.72 99.9 0.09 14.6 11 36696 0.5 42.9
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 2.04 2.15 99.2 1.24 1.5 7.1
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 2WX2 2.04 80.68 34827 1833 99.8 0.20195 0.19927 0.2047 0.25365 0.2571 RANDOM 43.54
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] -0.13 -0.13 -0.13 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_4_deg 22.358 r_dihedral_angle_3_deg 16.757 r_dihedral_angle_1_deg 6.456 r_mcangle_it 5.149 r_scbond_it 4.957 r_mcbond_it 3.825 r_mcbond_other 3.823 r_angle_refined_deg 1.963 r_angle_other_deg 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_4_deg 22.358 r_dihedral_angle_3_deg 16.757 r_dihedral_angle_1_deg 6.456 r_mcangle_it 5.149 r_scbond_it 4.957 r_mcbond_it 3.825 r_mcbond_other 3.823 r_angle_refined_deg 1.963 r_angle_other_deg 0.958 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 3529 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing