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THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% PEG 8000, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.627 α = 90 b = 133.627 β = 90 c = 101.67 γ = 120
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 2019-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915890 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 2.343 66.9 94 0.045 0.05 0.022 1 18.4 5.3 24281 74.8
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 2.343 2.481 52.5 1.176 1.301 0.556 0.585 1.4 5.5
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 3LWZ 2.343 66.9 23074 1226 85.45 0.1667 0.1643 0.1694 0.212 0.2108 RANDOM 82.799
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] 0.26 0.13 0.26 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.773 r_dihedral_angle_4_deg 21.144 r_dihedral_angle_3_deg 19.001 r_dihedral_angle_1_deg 7.426 r_angle_refined_deg 1.805 r_angle_other_deg 1.345 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.773 r_dihedral_angle_4_deg 21.144 r_dihedral_angle_3_deg 19.001 r_dihedral_angle_1_deg 7.426 r_angle_refined_deg 1.805 r_angle_other_deg 1.345 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4340 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 84
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction