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Crystal structure of human P-cadherin (monomer 1)
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 20% PEG 4,000
100 mM CaCl2
100 mM TRIS
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.84 α = 90 b = 40.91 β = 97.27 c = 72.48 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 210r 2013-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.5 26.22 91.2 0.054 13.1 3.4 32358
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 1.5 1.58 64.8 0.429 2.2 2.9
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 1.5 26.22 30742 1616 90.97 0.13953 0.13704 0.1415 0.18606 0.1916 RANDOM 21.136
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] 2.03 1.07 0.15 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.066 r_sphericity_free 22.738 r_dihedral_angle_4_deg 12.948 r_dihedral_angle_3_deg 11.22 r_sphericity_bonded 7.394 r_dihedral_angle_1_deg 6.602 r_rigid_bond_restr 4.496 r_angle_refined_deg 1.509 r_angle_other_deg 0.776 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.066 r_sphericity_free 22.738 r_dihedral_angle_4_deg 12.948 r_dihedral_angle_3_deg 11.22 r_sphericity_bonded 7.394 r_dihedral_angle_1_deg 6.602 r_rigid_bond_restr 4.496 r_angle_refined_deg 1.509 r_angle_other_deg 0.776 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1647 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing