☰ Navigation Tabs
Crystal structure of human P-cadherin (ss-dimer K14E)
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 26% PEG 4,000
170 lithium sulfate
15% glycerol
85 mM TRIS
Crystal Properties Matthews coefficient Solvent content 4.87 74.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.38 α = 90 b = 81.23 β = 105.79 c = 48.99 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 2013-12-16 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 2.48 42.43 98.3 0.061 13.8 3.5 15628
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 2.48 2.61 91.3 0.426 2.5 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 2.48 42.43 14868 760 98.12 0.20046 0.19863 0.204 0.23549 0.2413 RANDOM 53.379
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] 0.67 0.2 1.79 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_4_deg 14.808 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.026 r_long_range_B_other 6.015 r_scangle_other 4.611 r_mcangle_it 3.394 r_mcangle_other 3.393 r_scbond_it 2.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_4_deg 14.808 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.026 r_long_range_B_other 6.015 r_scangle_other 4.611 r_mcangle_it 3.394 r_mcangle_other 3.393 r_scbond_it 2.961 r_scbond_other 2.961 r_mcbond_other 2.263 r_mcbond_it 2.262 r_angle_refined_deg 1.598 r_angle_other_deg 0.798 r_chiral_restr 0.088 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 1639 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing