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Crystal Structure of Zebrafish Protocadherin-19 EC1-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 277 200 mM Sodium Chloride, 100 mM TrisHCl pH 8.1, 8% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.39 α = 90 b = 59.776 β = 94.39 c = 165.925 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 PIXEL DECTRIS PILATUS 200K 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-003 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.59 50 94.8 4.9 2.7 15416
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 3.59 3.66 86 0.386 2.1 2.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CO1 3.59 50 13943 652 93.97 0.24851 0.24588 0.2454 0.30498 0.3105 RANDOM 89.717
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] 0.43 0.47 -0.23 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.827 r_dihedral_angle_3_deg 19.381 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_1_deg 8.52 r_angle_refined_deg 1.466 r_angle_other_deg 0.985 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.827 r_dihedral_angle_3_deg 19.381 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_1_deg 8.52 r_angle_refined_deg 1.466 r_angle_other_deg 0.985 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6465 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing