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PCY1 in Complex with Follower Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 282 16% PEG 8,000, 0.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 14 mg/mL protein, Protein was preincubated with 5 mM boric acid and 1 mM PSA1 [14-32]
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.495 α = 87.41 b = 85.591 β = 78.28 c = 137.72 γ = 89.33
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 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97856 APS 21-ID-D
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 1.96 44.9 95.8 0.129 8.9 3.8 201248
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 1.96 1.967 96.8 0.525 3.3 3.9
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 1QFS 1.96 44.9 191296 9945 95.78 0.19068 0.18892 0.1952 0.22409 0.2292 RANDOM 19.961
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] 0.51 0.55 0.26 -0.45 -0.19 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.297 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 14.469 r_dihedral_angle_1_deg 6.545 r_long_range_B_refined 6.081 r_long_range_B_other 5.952 r_scangle_other 3.729 r_mcangle_it 2.71 r_mcangle_other 2.71 r_scbond_it 2.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.297 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 14.469 r_dihedral_angle_1_deg 6.545 r_long_range_B_refined 6.081 r_long_range_B_other 5.952 r_scangle_other 3.729 r_mcangle_it 2.71 r_mcangle_other 2.71 r_scbond_it 2.391 r_scbond_other 2.391 r_mcbond_it 1.825 r_mcbond_other 1.825 r_angle_refined_deg 1.684 r_angle_other_deg 1.461 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 22650 Nucleic Acid Atoms Solvent Atoms 2061 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing