5UW3

PCY1 in Complex with Follower Peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528216% 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 coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.495α = 87.41
b = 85.591β = 78.28
c = 137.72γ = 89.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97856APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9644.995.80.1298.93.8201248
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.961.96796.80.5253.33.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QFS1.9644.9191296994595.780.190680.188920.22409RANDOM19.961
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]
0.510.550.26-0.45-0.190.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.297
r_dihedral_angle_4_deg16.257
r_dihedral_angle_3_deg14.469
r_dihedral_angle_1_deg6.545
r_long_range_B_refined6.081
r_long_range_B_other5.952
r_scangle_other3.729
r_mcangle_it2.71
r_mcangle_other2.71
r_scbond_it2.391
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.297
r_dihedral_angle_4_deg16.257
r_dihedral_angle_3_deg14.469
r_dihedral_angle_1_deg6.545
r_long_range_B_refined6.081
r_long_range_B_other5.952
r_scangle_other3.729
r_mcangle_it2.71
r_mcangle_other2.71
r_scbond_it2.391
r_scbond_other2.391
r_mcbond_it1.825
r_mcbond_other1.825
r_angle_refined_deg1.684
r_angle_other_deg1.461
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.008
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 AtomsNumber
Protein Atoms22650
Nucleic Acid Atoms
Solvent Atoms2061
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing