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Crystal structure of mouse Protocadherin-15 EC1-2 BAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4APX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.02 M calcium chloride, 0.1 M sodium acetate, 30% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.88 57.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.616 α = 90 b = 99.616 β = 90 c = 58.56 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 PIXEL DECTRIS PILATUS 6M-F 2015-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.4 50 100 0.132 0.047 17.833 8.8 13043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 100 0.802 0.311 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4APX 2.4 49.86 12383 640 99.89 0.17326 0.17048 0.23289 0.2321 RANDOM 43.48
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] 1.18 0.59 1.18 -3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_1_deg 7.617 r_long_range_B_other 7.474 r_long_range_B_refined 7.471 r_scangle_other 5.696 r_mcangle_it 3.863 r_mcangle_other 3.862 r_scbond_it 3.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_1_deg 7.617 r_long_range_B_other 7.474 r_long_range_B_refined 7.471 r_scangle_other 5.696 r_mcangle_it 3.863 r_mcangle_other 3.862 r_scbond_it 3.428 r_scbond_other 3.417 r_mcbond_it 2.394 r_mcbond_other 2.39 r_angle_refined_deg 1.706 r_angle_other_deg 1.25 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 1826 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing