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Crystal structure of human P-cadherin (ss-X-dimer-long)
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 20% PEG 3,550
200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.64 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.21 α = 90 b = 105.83 β = 96.8 c = 90.21 γ = 90
Symmetry Space Group P 1 21 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 2012-10-27 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 2.7 43.31 99.1 0.09 10.2 3.4 43436
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 2.7 2.85 97.1 0.587 2 3.3
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 2.7 42.31 41234 2190 99.05 0.22933 0.22823 0.2313 0.24941 0.2493 RANDOM 56.351
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] 4.4 -1.68 -2.33 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.264 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_4_deg 12.331 r_dihedral_angle_1_deg 5.966 r_long_range_B_refined 3.503 r_long_range_B_other 3.503 r_scangle_other 2.188 r_mcangle_it 2.037 r_mcangle_other 2.037 r_angle_refined_deg 1.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.264 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_4_deg 12.331 r_dihedral_angle_1_deg 5.966 r_long_range_B_refined 3.503 r_long_range_B_other 3.503 r_scangle_other 2.188 r_mcangle_it 2.037 r_mcangle_other 2.037 r_angle_refined_deg 1.354 r_scbond_it 1.295 r_scbond_other 1.295 r_angle_other_deg 1.234 r_mcbond_other 1.196 r_mcbond_it 1.195 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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 9578 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing