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Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+ and 3-Hydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium phosphate dibasic, and 20 % polyethylene glycol 3350, 100 mM Tris buffer pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.579 α = 90 b = 88.315 β = 90 c = 162.97 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 RIGAKU HyPix-6000HE 2021-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.48 27.18 99.8 0.994 11.6 6.8 28203
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.54 99.8 0.904
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 3MOI 2.48 27.18 26742 1412 99.69 0.1943 0.1921 0.2351 0.216 RANDOM 21.005
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] -1.08 3.72 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.851 r_dihedral_angle_4_deg 20.375 r_dihedral_angle_3_deg 18.763 r_dihedral_angle_1_deg 7.289 r_angle_refined_deg 1.643 r_chiral_restr 0.116 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5336 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling MOLREP phasing