8R02

Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R17 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429320% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.5852.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.5α = 90
b = 140.83β = 90
c = 141.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2021-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91788DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.519.91999.70.99916.113.640494
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.550.597

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.519.91940436202199.7290.2050.20170.2639115.59
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]
5.565-3.074-2.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.753
r_dihedral_angle_3_deg17.184
r_dihedral_angle_6_deg13.914
r_lrange_it13.71
r_lrange_other13.71
r_scangle_it10.748
r_scangle_other10.747
r_mcangle_it9.957
r_mcangle_other9.956
r_scbond_it7.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.753
r_dihedral_angle_3_deg17.184
r_dihedral_angle_6_deg13.914
r_lrange_it13.71
r_lrange_other13.71
r_scangle_it10.748
r_scangle_other10.747
r_mcangle_it9.957
r_mcangle_other9.956
r_scbond_it7.041
r_scbond_other7.041
r_mcbond_it6.839
r_mcbond_other6.839
r_dihedral_angle_1_deg5.848
r_angle_refined_deg1.444
r_angle_other_deg0.804
r_nbd_other0.336
r_nbd_refined0.224
r_symmetry_nbd_other0.215
r_nbtor_refined0.18
r_symmetry_nbd_refined0.177
r_xyhbond_nbd_refined0.14
r_ncsr_local_group_20.113
r_symmetry_xyhbond_nbd_refined0.103
r_ncsr_local_group_10.097
r_symmetry_nbtor_other0.083
r_chiral_restr0.074
r_symmetry_xyhbond_nbd_other0.025
r_bond_refined_d0.008
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7729
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing