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Polyester Hydrolase Leipzig 7 (PHL7) bound to terephthalic acid (TPA) and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 50 mM Tris
100 mM KCl
30 % (v/v) PEG 400
10 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.352 α = 90 b = 56.069 β = 94.01 c = 100.442 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 RIGAKU HyPix-6000HE 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.5406
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 1.7 21.46 99.77 0.05707 0.06349 0.02696 0.997 19.81 4.9 63959
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 1.7 1.761 99.83 0.3389 0.4043 0.2168 0.838 3.02 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS FREE R-VALUE 7NEI 1.7 21.46 1.34 63957 2885 99.84 0.1309 0.1295 0.1296 0.1605 0.1603 copied from PDB ID: 7NEI
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 f_dihedral_angle_d 12.434 f_angle_d 0.956 f_chiral_restr 0.056 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3936 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling Coot model building