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Crystal Structure of a Cutinase from Saccharopolyspora Dendranthemae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 Crystals were grown by sitting drop vapor diffusion at 4 degrees C. Drops were set up by mixing 1 uL of protein solution (10 mg/mL in Y sodium phosphate buffer, pH 7.5) with 1 uL of reservoir solution (0.2 M Sodium Fluoride, 20% (w/v) PEG 3350, unbuffered). The drops were incubated for 9 months. The setup was performed using a TTP Labtech Mosquito liquid handling robot.
Crystal Properties Matthews coefficient Solvent content 1.83 32.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.502 α = 90 b = 61.707 β = 90 c = 88.128 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 EIGER X 16M 2024-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.13 50.55 84.1 0.057 0.06 0.99 21.8 11.1 67263
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.2 11.2 0.5 0.65 0.65 1.4
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 1.13 50.55 63583 3358 83.68 0.12105 0.11981 0.12 0.14444 0.1457 RANDOM 8.843
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] 1.12 -1.27 0.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.902 r_long_range_B_other 11.298 r_dihedral_angle_3_deg 11.221 r_dihedral_angle_2_deg 7.958 r_scangle_other 6.742 r_dihedral_angle_1_deg 6.341 r_scbond_it 4.887 r_scbond_other 4.885 r_mcangle_other 4.389 r_mcangle_it 4.384
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.902 r_long_range_B_other 11.298 r_dihedral_angle_3_deg 11.221 r_dihedral_angle_2_deg 7.958 r_scangle_other 6.742 r_dihedral_angle_1_deg 6.341 r_scbond_it 4.887 r_scbond_other 4.885 r_mcangle_other 4.389 r_mcangle_it 4.384 r_rigid_bond_restr 4.288 r_mcbond_it 3.043 r_mcbond_other 3.02 r_angle_refined_deg 1.834 r_angle_other_deg 0.639 r_chiral_restr 0.111 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 1913 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement autoPROC data scaling autoPROC data reduction PHASER phasing PDB_EXTRACT data extraction