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High resolution crystal structure of a Leaf-branch compost cutinase quintuple variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 285 0.1 M Imidazole, 1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.413 α = 90 b = 109.413 β = 90 c = 35.183 γ = 120
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 PILATUS 6M 2018-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.14 94.75 100 0.102 11.2 9.5 87457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.16 100 1.051 0.364 0.744 2.1 9.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4EB0 1.14 94.75 83089 4368 99.99 0.1143 0.1132 0.1131 0.1365 0.1371 RANDOM 15.815
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] -0.06 -0.03 -0.06 0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 32.087 r_dihedral_angle_2_deg 28.409 r_dihedral_angle_1_deg 24.794 r_sphericity_free 21.226 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_3_deg 9.403 r_rigid_bond_restr 7.486 r_angle_refined_deg 1.844 r_angle_other_deg 1.213 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 32.087 r_dihedral_angle_2_deg 28.409 r_dihedral_angle_1_deg 24.794 r_sphericity_free 21.226 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_3_deg 9.403 r_rigid_bond_restr 7.486 r_angle_refined_deg 1.844 r_angle_other_deg 1.213 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1948 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction