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Crystal structure of phenylpyruvate reductase from Lactobacillus sp. CGMCC 9967
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 3.5 293.15 PEG 1000, Citric acid, B-Nicotinamide adeinie dinucleotide
Crystal Properties Matthews coefficient Solvent content 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.896 α = 90 b = 48.97 β = 116.72 c = 89.896 γ = 90
Symmetry Space Group P 1 21 1
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 Bruker PHOTON II 2022-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.89 23.49 86.7394 0.141 0.062 7.29 2 3064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.89 4.47 54.7 0.371 0.748 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.895 23.49 2909 141 86.7394 0.25875 0.25755 0.2075 0.2795 0.2325 RANDOM 42.129
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] -87.97 25.56 131.05 -43.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.123 r_dihedral_angle_4_deg 15.592 r_dihedral_angle_3_deg 14.599 r_long_range_B_refined 7.974 r_long_range_B_other 7.974 r_dihedral_angle_1_deg 7.64 r_mcangle_it 6.093 r_mcangle_other 6.091 r_scangle_other 4.649 r_mcbond_it 4.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.123 r_dihedral_angle_4_deg 15.592 r_dihedral_angle_3_deg 14.599 r_long_range_B_refined 7.974 r_long_range_B_other 7.974 r_dihedral_angle_1_deg 7.64 r_mcangle_it 6.093 r_mcangle_other 6.091 r_scangle_other 4.649 r_mcbond_it 4.351 r_mcbond_other 4.35 r_scbond_it 3.221 r_scbond_other 3.221 r_rigid_bond_restr 1.976 r_angle_refined_deg 1.532 r_angle_other_deg 1.016 r_chiral_restr 0.046 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4680 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement HKL-2000 data reduction SHELXCD phasing