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Bicyclic INCYPRO Pseudomonas fluorescens esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 293 100 mM CHES pH10
25 % (w/v) PEG3000
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.8 α = 90 b = 146.25 β = 122.63 c = 154.59 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS EIGER2 XE 16M 2021-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.5 99 99.8 0.997 8.88 14.1 164678
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 2.5 2.6 99.9 0.521 1.12
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 2.5 77.72 156444 8234 99.99 0.1842 0.18213 0.1821 0.22349 0.2235 RANDOM 70.412
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] -0.09 0.26 1.19 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 5.476 r_dihedral_angle_2_deg 4.894 r_long_range_B_refined 4.596 r_mcangle_it 2.003 r_scbond_it 1.781 r_mcbond_it 1.226 r_angle_refined_deg 0.868 r_chiral_restr 0.076 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 5.476 r_dihedral_angle_2_deg 4.894 r_long_range_B_refined 4.596 r_mcangle_it 2.003 r_scbond_it 1.781 r_mcbond_it 1.226 r_angle_refined_deg 0.868 r_chiral_restr 0.076 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31861 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 420
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB-REDO refinement