☰ Navigation Tabs
Crystal Structure of Human Protocadherin-24 EC1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 0.2 M MgCl
0.1 M HEPES pH 7.3
10% PEF 4000
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.879 α = 90 b = 119.769 β = 104.12 c = 74.318 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 6M-F 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 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 2.3 50 95.5 10.9 3.1 50945
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 2.3 2.34 80.3 0.255 3 2.6
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 5CYX 2.3 50 48462 2458 95.17 0.20617 0.20463 0.2095 0.23546 0.2411 RANDOM 40.633
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] -0.07 -0.32 0.3 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.906 r_dihedral_angle_4_deg 25.146 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_1_deg 7.311 r_long_range_B_refined 5.78 r_long_range_B_other 5.775 r_scangle_other 3.797 r_mcangle_it 3.337 r_mcangle_other 3.337 r_scbond_it 2.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.906 r_dihedral_angle_4_deg 25.146 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_1_deg 7.311 r_long_range_B_refined 5.78 r_long_range_B_other 5.775 r_scangle_other 3.797 r_mcangle_it 3.337 r_mcangle_other 3.337 r_scbond_it 2.342 r_scbond_other 2.342 r_mcbond_it 2.056 r_mcbond_other 2.052 r_angle_refined_deg 1.46 r_angle_other_deg 1.23 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.006 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 6610 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing