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X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125, ALTERNATIVE CRYSTAL FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IVY PDB ENTRY 3IVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS, PH 5.5, 17% PEG 10000 AT 4 C
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.48 α = 90 b = 74.578 β = 90 c = 102.225 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 CCD MIRRORS 2010-01-15 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 1.48 102.6 94.9 0.07 9.5 4.1 66632 1.5 15
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 1.48 1.56 71.6 0.55 1.5 1.9
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 3IVY 1.48 102.22 63143 3367 94.73 0.15315 0.15052 0.1472 0.20179 0.1998 RANDOM 18.624
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] 0.2 0.14 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 13.093 r_sphericity_free 10.468 r_sphericity_bonded 6.721 r_scangle_it 6.275 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.542 r_mcangle_it 3.095 r_rigid_bond_restr 2.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 13.093 r_sphericity_free 10.468 r_sphericity_bonded 6.721 r_scangle_it 6.275 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.542 r_mcangle_it 3.095 r_rigid_bond_restr 2.703 r_mcbond_it 2.182 r_angle_refined_deg 1.97 r_chiral_restr 0.171 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 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 3259 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing