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THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM PROPIONIBACTERIUM ACNES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2 M Ammonium sulphate, 0.2 M sodium chloride, 0.1M TRIS pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.82 α = 90 b = 128.82 β = 90 c = 75.999 γ = 120
Symmetry Space Group P 3 2 1
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 S 6M 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.66 64.41 95.8 0.089 0.096 0.035 0.999 12.5 7.7 71997 31.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.77 64.6 1.34 1.442 0.527 0.511 1.5 7.3
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 3N7A 1.7 64.41 68108 3629 89.74 0.1524 0.1513 0.159 0.1742 0.1798 RANDOM 28.437
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] 0.69 0.69 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.922 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.592 r_angle_other_deg 1.437 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.922 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.592 r_angle_other_deg 1.437 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4375 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction