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Crystal structure of human P-cadherin (ss-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 31% PEG 400
15 mM CaCl2
5% glycerol
Crystal Properties Matthews coefficient Solvent content 4.89 74.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.95 α = 90 b = 80.91 β = 105.75 c = 49.18 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 1.85 40.46 99.9 0.066 14.5 5.5 38255
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 1.85 1.95 100 0.635 2.6 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZMN 1.85 40.46 36701 1553 99.84 0.19621 0.1953 0.21775 0.2278 RANDOM 42.601
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] -0.16 0.46 2.44 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_3_deg 12.118 r_dihedral_angle_4_deg 9.728 r_long_range_B_refined 7.265 r_long_range_B_other 7.101 r_dihedral_angle_1_deg 6.769 r_scangle_other 4.781 r_scbond_it 3.242 r_scbond_other 3.226 r_mcangle_other 2.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_3_deg 12.118 r_dihedral_angle_4_deg 9.728 r_long_range_B_refined 7.265 r_long_range_B_other 7.101 r_dihedral_angle_1_deg 6.769 r_scangle_other 4.781 r_scbond_it 3.242 r_scbond_other 3.226 r_mcangle_other 2.882 r_mcangle_it 2.879 r_mcbond_it 2.091 r_mcbond_other 2.086 r_angle_refined_deg 1.764 r_angle_other_deg 0.802 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1639 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing