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The structure of a carbohydrate active P450
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L90 5l90, 4ubs, 1cl6 and 3ejd experimental model PDB 4UBS 5l90, 4ubs, 1cl6 and 3ejd experimental model PDB 1CL6 5l90, 4ubs, 1cl6 and 3ejd experimental model PDB 3EJD 5l90, 4ubs, 1cl6 and 3ejd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 20% PEG 3350, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.28 α = 90 b = 68.152 β = 90 c = 199.728 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 100 PIXEL DECTRIS PILATUS 6M-F 2017-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.7 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.25 99.87 99.5 0.111 14.4 10 418105 41766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 99.7 0.809 3.3
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 5l90, 4ubs, 1cl6 and 3ejd 2.25 99.86 39595 2099 99.44 0.20708 0.20492 0.2108 0.24802 0.253 RANDOM 36.124
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] -0.8 0.93 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.189 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.911 r_long_range_B_refined 6.835 r_long_range_B_other 6.832 r_dihedral_angle_1_deg 5.976 r_scangle_other 5.237 r_mcangle_it 4.168 r_mcangle_other 4.168 r_scbond_it 3.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.189 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.911 r_long_range_B_refined 6.835 r_long_range_B_other 6.832 r_dihedral_angle_1_deg 5.976 r_scangle_other 5.237 r_mcangle_it 4.168 r_mcangle_other 4.168 r_scbond_it 3.328 r_scbond_other 3.328 r_mcbond_it 2.832 r_mcbond_other 2.831 r_angle_refined_deg 1.556 r_angle_other_deg 0.865 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5906 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing