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Crystal Structure of Human Protocadherin-1 EC3-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES pH 6.5, 20% PEG 4000, 0.6 M Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 3.38 63.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.569 α = 90 b = 125.569 β = 90 c = 45.294 γ = 90
Symmetry Space Group P 42 21 2
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 2016-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97921 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.05 50 99.3 0.166 0.175 0.054 0.938 12 9.9 7363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.1 90.6 1.027 1.11 0.401 0.551 1.67 6.5
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 5DZV 3.05 44.43 6899 334 98.61 0.22201 0.21991 0.2228 0.26614 0.2652 RANDOM 59.372
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] 1.31 1.31 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_3_deg 18.141 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_1_deg 9.645 r_long_range_B_refined 6.481 r_long_range_B_other 6.475 r_scangle_other 3.551 r_mcangle_it 3.209 r_mcangle_other 3.209 r_scbond_it 2.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_3_deg 18.141 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_1_deg 9.645 r_long_range_B_refined 6.481 r_long_range_B_other 6.475 r_scangle_other 3.551 r_mcangle_it 3.209 r_mcangle_other 3.209 r_scbond_it 2.154 r_scbond_other 2.15 r_mcbond_it 1.955 r_mcbond_other 1.943 r_angle_refined_deg 1.536 r_angle_other_deg 1.189 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 1533 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing