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Crystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in ligand free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VE4 PDB ENTRY 2VE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 PEG 3350, POTASSIUM PHOSPHATE, n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.823 α = 74.21 b = 79.874 β = 81.56 c = 117.146 γ = 68.49
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 MARMOSAIC 225 mm CCD Be Lenses/Diamond Laue Mono 2008-11-01 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F 2 SYNCHROTRON APS BEAMLINE 21-ID-D 1.73892 APS 21-ID-D
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 1.89 30 97.8 0.06 18.5 4 153658 150278 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.89 1.97 96.7 0.472 0.472 3.1 3.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION combination of MR and Fe-SAD THROUGHOUT PDB ENTRY 2VE4 1.89 28.62 146460 142726 7519 97.45 0.19716 0.19522 0.1934 0.23423 0.231 RANDOM 36.415
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] 0.03 -0.2 0.14 0.02 -0.01 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.719 r_dihedral_angle_4_deg 20.034 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.346 r_scangle_it 5.553 r_scbond_it 3.583 r_mcangle_it 2.196 r_angle_refined_deg 1.894 r_mcbond_it 1.32 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.719 r_dihedral_angle_4_deg 20.034 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.346 r_scangle_it 5.553 r_scbond_it 3.583 r_mcangle_it 2.196 r_angle_refined_deg 1.894 r_mcbond_it 1.32 r_chiral_restr 0.149 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14192 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 172
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling