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Crystal structure of human P-cadherin (ss-dimer Q101L)
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 30% PEG 400
150 mM CaCl2
5% glycerol
95 mM HEPES
Crystal Properties Matthews coefficient Solvent content 4.79 74.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.7 α = 90 b = 77.99 β = 105.78 c = 49.23 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 2.15 35.74 95.2 0.085 8.6 3.5 22729
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 2.15 2.27 89.7 0.49 2.3 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 2.15 35.74 21587 1127 94.7 0.22343 0.22192 0.227 0.25199 0.253 RANDOM 54.505
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] -0.09 1.26 2.19 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 23.29 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_1_deg 7.585 r_long_range_B_refined 7.566 r_long_range_B_other 7.529 r_scangle_other 4.346 r_mcangle_it 3.392 r_mcangle_other 3.392 r_scbond_it 2.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 23.29 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_1_deg 7.585 r_long_range_B_refined 7.566 r_long_range_B_other 7.529 r_scangle_other 4.346 r_mcangle_it 3.392 r_mcangle_other 3.392 r_scbond_it 2.854 r_scbond_other 2.854 r_mcbond_it 2.395 r_mcbond_other 2.374 r_angle_refined_deg 2.003 r_angle_other_deg 0.904 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1638 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing