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Human P-cadherin MEC1 with scFv TSP7 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QOK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200 mM potassium phosphate monobasic,
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.57 α = 90 b = 49.41 β = 101.89 c = 111.66 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 315 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.55 109.26 99.1 0.125 0.994 10.4 5.4 23310
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 2.55 2.69 96.3 0.67 2.4 5.2
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 1QOK 2.55 109.26 22077 1222 98.76 0.21693 0.2141 0.217 0.2709 0.2709 RANDOM 43.579
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] 0.75 1.69 -1.1 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_3_deg 15.941 r_dihedral_angle_4_deg 14.241 r_dihedral_angle_1_deg 6.637 r_long_range_B_refined 3.507 r_long_range_B_other 3.393 r_scangle_other 1.776 r_mcangle_it 1.729 r_mcangle_other 1.729 r_angle_refined_deg 1.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_3_deg 15.941 r_dihedral_angle_4_deg 14.241 r_dihedral_angle_1_deg 6.637 r_long_range_B_refined 3.507 r_long_range_B_other 3.393 r_scangle_other 1.776 r_mcangle_it 1.729 r_mcangle_other 1.729 r_angle_refined_deg 1.291 r_scbond_it 1.046 r_scbond_other 1.028 r_mcbond_it 0.992 r_mcbond_other 0.992 r_angle_other_deg 0.955 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 4998 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER model building