5JYL

Human P-cadherin MEC1 with scFv TSP7 bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293200 mM potassium phosphate monobasic, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4750.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.57α = 90
b = 49.41β = 101.89
c = 111.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.55109.2699.10.1250.99410.45.423310
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6996.30.672.45.2

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 REPLACEMENTTHROUGHOUT1QOK2.55109.2622077122298.760.216930.21410.2709RANDOM43.579
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]
0.751.69-1.1-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.13
r_dihedral_angle_3_deg15.941
r_dihedral_angle_4_deg14.241
r_dihedral_angle_1_deg6.637
r_long_range_B_refined3.507
r_long_range_B_other3.393
r_scangle_other1.776
r_mcangle_it1.729
r_mcangle_other1.729
r_angle_refined_deg1.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.13
r_dihedral_angle_3_deg15.941
r_dihedral_angle_4_deg14.241
r_dihedral_angle_1_deg6.637
r_long_range_B_refined3.507
r_long_range_B_other3.393
r_scangle_other1.776
r_mcangle_it1.729
r_mcangle_other1.729
r_angle_refined_deg1.291
r_scbond_it1.046
r_scbond_other1.028
r_mcbond_it0.992
r_mcbond_other0.992
r_angle_other_deg0.955
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms4998
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERmodel building