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The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, crystal form 2
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, HANGING DROP 6.5 293 2M sodium chloride, 0.2M sodium tartrate, 0.1M MOPS pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.28 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.572 α = 90 b = 137.948 β = 90 c = 139.417 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 PILATUS3 6M 2018-02-25 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 1.6 137.57 99.7 0.107 0.12 0.052 0.993 7.3 5.5 346154
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 1.6 1.63 98.4 3.327 3.688 1.563 0.168 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6HSQ 1.6 79.98 328295 17403 99.64 0.1919 0.1911 0.2077 0.2181 RANDOM 33.889
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] 0.95 0.34 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.412 r_dihedral_angle_4_deg 20.073 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.552 r_angle_refined_deg 1.828 r_angle_other_deg 1.529 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.412 r_dihedral_angle_4_deg 20.073 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.552 r_angle_refined_deg 1.828 r_angle_other_deg 1.529 r_chiral_restr 0.101 r_bond_refined_d 0.014 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 13969 Nucleic Acid Atoms Solvent Atoms 1412 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement Aimless data scaling AMoRE phasing PDB_EXTRACT data extraction XDS data reduction