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X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP124 in complex with phytanic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WM5 PDB ENTRY 2WM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 21% PEG4000, 0.1 M BIS-TRIS, PH 5.5, 0.2 M CALCIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.16 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.596 α = 90 b = 73.4 β = 90 c = 109.696 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 110 CCD ADSC QUANTUM 315r MIRRORS 2009-01-24 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 2.1 50 97 0.09 30.8 6.2 24784 29.1
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 2.1 2.14 76.6 0.53 3.6 4
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 2WM5 2.11 43.94 22780 1197 96.77 0.169 0.16561 0.1674 0.23189 0.2325 RANDOM 29.366
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] -2.16 1.98 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.94 r_dihedral_angle_4_deg 19.616 r_dihedral_angle_3_deg 16.844 r_sphericity_free 8.668 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.524 r_sphericity_bonded 3.963 r_scbond_it 3.055 r_rigid_bond_restr 2.045 r_mcangle_it 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.94 r_dihedral_angle_4_deg 19.616 r_dihedral_angle_3_deg 16.844 r_sphericity_free 8.668 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.524 r_sphericity_bonded 3.963 r_scbond_it 3.055 r_rigid_bond_restr 2.045 r_mcangle_it 2.002 r_angle_refined_deg 1.907 r_mcbond_it 1.231 r_chiral_restr 0.145 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing