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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-(3,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C0C PDB ENTRY 4C0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.3 M AMMONIUM SULFATE, 0.1 M BIS- TRIS, PH 5.5; 19% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.394 α = 90 b = 128.394 β = 90 c = 116.573 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 MARRESEARCH MIRRORS 2014-03-26 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 2.43 116.57 100 0.17 11.7 12.8 21961 0.5 58.7
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 2.43 2.56 100 1.99 1.5 13.1
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 4C0C 2.43 111.19 20808 1125 99.95 0.19715 0.1944 0.198 0.24651 0.2475 RANDOM 52.233
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] -0.72 -0.72 -0.72 2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_3_deg 18.089 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_1_deg 6.22 r_mcangle_it 5.339 r_scbond_it 4.797 r_mcbond_other 3.587 r_mcbond_it 3.586 r_angle_refined_deg 1.594 r_angle_other_deg 0.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_3_deg 18.089 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_1_deg 6.22 r_mcangle_it 5.339 r_scbond_it 4.797 r_mcbond_other 3.587 r_mcbond_it 3.586 r_angle_refined_deg 1.594 r_angle_other_deg 0.852 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 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 3509 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing