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The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, 40% ethanol as cryoprotectant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% ME2K PEG, 0.1M Lithium sulphate, 0.1M HEPES pH 7.5. Cryoprotected with 40% ethanol vapour diffused into the crystallisation well.
Crystal Properties Matthews coefficient Solvent content 3.32 62.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.828 α = 90 b = 138.828 β = 90 c = 138.828 γ = 90
Symmetry Space Group P 21 3
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 0.915870 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 69.51 94.6 0.053 0.057 0.017 0.999 19.7 10 56976
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 2.057 60.1 2.033 2.143 0.676 0.77 1.3 10.2
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 6HSQ 2 69.51 54128 2836 94.53 0.1742 0.1731 0.1812 0.1943 0.1996 RANDOM 86.399
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 39.915 r_dihedral_angle_3_deg 17.827 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_1_deg 7.876 r_angle_refined_deg 2.528 r_angle_other_deg 1.685 r_chiral_restr 0.124 r_bond_refined_d 0.024 r_gen_planes_refined 0.016 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.915 r_dihedral_angle_3_deg 17.827 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_1_deg 7.876 r_angle_refined_deg 2.528 r_angle_other_deg 1.685 r_chiral_restr 0.124 r_bond_refined_d 0.024 r_gen_planes_refined 0.016 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4672 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction