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Crystal structure of human P-cadherin (ss-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 7.5 293 28% PEG 400
250 mM CaCl2
HEPES 100 mM
Crystal Properties Matthews coefficient Solvent content 4.19 70.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.09 α = 90 b = 182.09 β = 90 c = 41.04 γ = 120
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 2012-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 2.2 39.72 94.6 0.078 18.2 9.2 37841
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 2.2 2.32 70.7 0.387 4.4 6.3
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 2.2 39.72 35936 1897 94.14 0.18861 0.18645 0.1912 0.23112 0.2378 RANDOM 45.968
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] 0.61 0.31 0.61 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.551 r_dihedral_angle_3_deg 14.797 r_dihedral_angle_4_deg 10.041 r_dihedral_angle_1_deg 7.142 r_long_range_B_refined 6.283 r_long_range_B_other 6.258 r_scangle_other 3.481 r_mcangle_it 2.99 r_mcangle_other 2.989 r_scbond_it 2.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.551 r_dihedral_angle_3_deg 14.797 r_dihedral_angle_4_deg 10.041 r_dihedral_angle_1_deg 7.142 r_long_range_B_refined 6.283 r_long_range_B_other 6.258 r_scangle_other 3.481 r_mcangle_it 2.99 r_mcangle_other 2.989 r_scbond_it 2.225 r_scbond_other 2.217 r_mcbond_it 1.86 r_mcbond_other 1.86 r_angle_refined_deg 1.603 r_angle_other_deg 0.798 r_chiral_restr 0.093 r_bond_refined_d 0.014 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 3189 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing