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Crystal Structure of Zebrafish Protocadherin-19 EC3-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AQE 4aqe_A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 277 100 mM Sodium Cacodylate pH 6.1, 100 mM Calcium Acetate, 25% MPD
Crystal Properties Matthews coefficient Solvent content 3.88 68.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.355 α = 90 b = 86.631 β = 122.13 c = 132.583 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 PIXEL DECTRIS PILATUS 6M-F 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 2.51 50 98 16.59 4.4 47847
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 2.51 2.55 88.1 0.591 2.21 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4aqe_A 2.51 50 45487 2360 97.78 0.19091 0.18837 0.23943 0.2679 RANDOM 77.112
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] -0.14 0.1 -0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.003 r_dihedral_angle_4_deg 21.534 r_dihedral_angle_3_deg 20.289 r_long_range_B_other 14.153 r_long_range_B_refined 14.152 r_scangle_other 10.243 r_dihedral_angle_1_deg 10.03 r_mcangle_it 9.708 r_mcangle_other 9.707 r_scbond_it 6.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.003 r_dihedral_angle_4_deg 21.534 r_dihedral_angle_3_deg 20.289 r_long_range_B_other 14.153 r_long_range_B_refined 14.152 r_scangle_other 10.243 r_dihedral_angle_1_deg 10.03 r_mcangle_it 9.708 r_mcangle_other 9.707 r_scbond_it 6.549 r_scbond_other 6.545 r_mcbond_other 6.261 r_mcbond_it 6.26 r_angle_refined_deg 1.392 r_angle_other_deg 0.74 r_chiral_restr 0.099 r_gen_planes_refined 0.015 r_bond_refined_d 0.011 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 6464 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing