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Crystal structure of human P-cadherin (int-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 25% PEG 4,000
10% 2-isopropanol
HEPES 100 mM
Crystal Properties Matthews coefficient Solvent content 4.18 70.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.46 α = 90 b = 181.46 β = 90 c = 40.73 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 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 3.1 43.59 99.5 0.115 3.4 3.4 14283
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 3.1 3.27 98.6 0.407 3 3.1
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 3.1 43.59 13559 717 99.29 0.20755 0.20608 0.2101 0.23538 0.2372 RANDOM 60.368
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] 1.06 0.53 1.06 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.262 r_dihedral_angle_4_deg 12.885 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.63 r_long_range_B_refined 2.808 r_long_range_B_other 2.808 r_mcangle_it 1.132 r_mcangle_other 1.131 r_angle_refined_deg 0.927 r_scangle_other 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.262 r_dihedral_angle_4_deg 12.885 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.63 r_long_range_B_refined 2.808 r_long_range_B_other 2.808 r_mcangle_it 1.132 r_mcangle_other 1.131 r_angle_refined_deg 0.927 r_scangle_other 0.884 r_angle_other_deg 0.653 r_mcbond_it 0.619 r_mcbond_other 0.619 r_scbond_it 0.477 r_scbond_other 0.477 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 3081 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing