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PCY1 in Complex with Follower Peptide and Covalent Inhibitor ZPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 282 20% PEG 8,000, 0.1 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 10 mg/mL protein, Protein was preincubated with 1 mm ZPP and 1 mM PSA1 [27-32]
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.508 α = 87.6 b = 85.456 β = 78.17 c = 138.123 γ = 89.38
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.3 45.2 98.9 0.13 10.2 3.9 43560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.311 99.5 0.279 5 3.9
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 THROUGHOUT 3.3 45.2 41469 2089 98.88 0.17473 0.17247 0.1732 0.21969 0.2151 RANDOM 33.104
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] 1.59 1.87 0.11 -2.14 -2.07 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.312 r_long_range_B_refined 5.717 r_long_range_B_other 5.717 r_scangle_other 3.536 r_mcangle_it 3.472 r_mcangle_other 3.472 r_scbond_it 2.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.312 r_long_range_B_refined 5.717 r_long_range_B_other 5.717 r_scangle_other 3.536 r_mcangle_it 3.472 r_mcangle_other 3.472 r_scbond_it 2.031 r_scbond_other 2.031 r_mcbond_it 2.029 r_mcbond_other 2.029 r_angle_refined_deg 1.475 r_angle_other_deg 1.168 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22624 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing