9FIX | pdb_00009fix

MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BW8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2982.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.9174.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.796α = 90
b = 125.796β = 90
c = 73.766γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 12M2017-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9677DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.7847.9199.70.110.110.03519.820.816878
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.782.931.751.840.562.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.7847.911601884299.530.198430.196620.20730.233420.2326RANDOM87.539
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]
0.180.090.18-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.861
r_long_range_B_refined16.943
r_long_range_B_other16.941
r_scangle_other14.036
r_mcangle_other11.293
r_mcangle_it11.289
r_dihedral_angle_2_deg10.453
r_scbond_it9.9
r_scbond_other9.897
r_dihedral_angle_1_deg9.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.861
r_long_range_B_refined16.943
r_long_range_B_other16.941
r_scangle_other14.036
r_mcangle_other11.293
r_mcangle_it11.289
r_dihedral_angle_2_deg10.453
r_scbond_it9.9
r_scbond_other9.897
r_dihedral_angle_1_deg9.281
r_mcbond_other8.314
r_mcbond_it8.313
r_angle_refined_deg1.884
r_angle_other_deg0.616
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms2089
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling