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Crystal Structure of Lizard Cadherin-23 EC1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES pH 6.5
1.1 M CaCl2
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.386 α = 90 b = 43.386 β = 90 c = 296.227 γ = 90
Symmetry Space Group P 41 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 2016-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.097 50 98.3 0.106 16.65 6.5 17931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.097 2.14 86 0.589
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WHV 2.097 41.671 17565 891 98.475 0.214 0.2108 0.2173 0.2665 0.2648 40.331
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] 1.921 1.921 -3.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 17.002 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 7.924 r_lrange_it 6.67 r_lrange_other 6.252 r_scangle_other 3.219 r_scangle_it 3.218 r_mcangle_it 2.797 r_mcangle_other 2.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 17.002 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 7.924 r_lrange_it 6.67 r_lrange_other 6.252 r_scangle_other 3.219 r_scangle_it 3.218 r_mcangle_it 2.797 r_mcangle_other 2.796 r_scbond_it 2.011 r_scbond_other 2.008 r_angle_refined_deg 1.857 r_mcbond_other 1.774 r_mcbond_it 1.773 r_angle_other_deg 1.396 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.218 r_metal_ion_refined 0.209 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.172 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1613 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing