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Crystal structure of human P-cadherin (enc-X-dimer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.15 M Lithium sulfate
7.5 mM nickel sulfate
100 mM TRIS
Crystal Properties Matthews coefficient Solvent content 4.16 70.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.369 α = 90 b = 106.81 β = 94.86 c = 77.579 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 2014-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 47.02 98.8 0.066 15.4 5 33629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 92 0.279 4.8 4.3
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 4ZMN 2.3 47.02 31831 1798 98.72 0.23277 0.23036 0.2351 0.27558 0.2783 RANDOM 37.492
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] -0.71 0.29 -2.43 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.326 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_4_deg 10.384 r_dihedral_angle_1_deg 7.007 r_long_range_B_refined 6.799 r_long_range_B_other 6.7 r_scangle_other 4.471 r_mcangle_it 4.062 r_mcangle_other 4.061 r_scbond_it 3.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.326 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_4_deg 10.384 r_dihedral_angle_1_deg 7.007 r_long_range_B_refined 6.799 r_long_range_B_other 6.7 r_scangle_other 4.471 r_mcangle_it 4.062 r_mcangle_other 4.061 r_scbond_it 3.278 r_scbond_other 2.805 r_mcbond_it 2.569 r_mcbond_other 2.568 r_angle_refined_deg 1.592 r_angle_other_deg 0.804 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3274 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing