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EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z1929757385
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IBE 6IBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 0.075M ammonium nitrate, 0.1M MES pH 6.0, 6.5% PEG 2000, 6.5% PEG 3350, 6.5% PEG 4000, 6.5% PEG 5000, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.58 α = 90 b = 77.01 β = 90 c = 99.88 γ = 90
Symmetry Space Group P 21 21 21
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 2019-07-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.63 41.9 99.9 0.084 0.092 0.036 0.998 11.1 6.2 38029
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 1.63 1.67 100 1.257 1.398 0.6 0.521 5.3 2788
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 FOURIER SYNTHESIS THROUGHOUT 6IBE 1.63 41.94 36065 1898 99.86 0.2149 0.2132 0.2328 0.2473 0.2611 RANDOM 30.659
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] -0.21 0.9 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 16.388 r_dihedral_angle_1_deg 7.03 r_mcangle_it 3.497 r_mcbond_other 2.209 r_mcbond_it 2.208 r_angle_refined_deg 1.542 r_angle_other_deg 1.331 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 16.388 r_dihedral_angle_1_deg 7.03 r_mcangle_it 3.497 r_mcbond_other 2.209 r_mcbond_it 2.208 r_angle_refined_deg 1.542 r_angle_other_deg 1.331 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2335 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing