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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 6G5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 % PEG 3350
150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.024 α = 90 b = 67.878 β = 90 c = 199.653 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 2.4 99.84 99.9 0.127 10.1 6.8 233876 34391
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 2.4 2.49 0.789 2.4
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 6G5O 2.4 99.83 32657 1669 99.81 0.17403 0.17182 0.1726 0.2167 0.2174 RANDOM 38.169
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] -0.57 -0.49 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 17.761 r_dihedral_angle_3_deg 15.168 r_long_range_B_refined 8.251 r_dihedral_angle_1_deg 5.921 r_mcangle_it 4.397 r_scbond_it 4.218 r_mcbond_it 2.93 r_angle_refined_deg 1.602 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 17.761 r_dihedral_angle_3_deg 15.168 r_long_range_B_refined 8.251 r_dihedral_angle_1_deg 5.921 r_mcangle_it 4.397 r_scbond_it 4.218 r_mcbond_it 2.93 r_angle_refined_deg 1.602 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_it r_scangle_other 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 5972 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing