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The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1M Lithium Sulphate, 0.1M MOPS pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.386 α = 90 b = 139.386 β = 90 c = 139.386 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 6M 2018-03-12 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 1.456 98.561 95.9 0.084 0.12 0.028 0.999 14.6 9.9 150335 22.5
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 1.456 1.496 62.6 1.546 1.636 0.532 0.536 9.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RC9 1.46 98.56 142816 7523 95.89 0.169 0.1682 0.1858 0.1983 RANDOM 25.658
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 40.131 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 12.775 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.151 r_angle_other_deg 1.625 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.131 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 12.775 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.151 r_angle_other_deg 1.625 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4656 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction