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Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). Crystals suitable for diffraction experiments were obtained by sitting drop vapour diffusion at 277 K in 400 nL drops containing equal volumes of protein and a solution containing 30% PEG 2K MME and 0.1 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.908 α = 90 b = 79.908 β = 90 c = 144.712 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 X 2M 2012-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917 Diamond I04-1
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 1.65 26.82 99.93 0.061 15.4 12.1 53715
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 1.65 1.7 100 0.783 3.8 12.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 1.65 26.82 53715 2872 99.93 0.16493 0.16341 0.1746 0.19359 0.2054 RANDOM 15.861
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 12.778 r_dihedral_angle_1_deg 6.549 r_angle_refined_deg 2.23 r_angle_other_deg 1.017 r_chiral_restr 0.158 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 12.778 r_dihedral_angle_1_deg 6.549 r_angle_refined_deg 2.23 r_angle_other_deg 1.017 r_chiral_restr 0.158 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 2733 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MLPHARE phasing