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EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z2856434868
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 2.23 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.53 α = 90 b = 77.55 β = 90 c = 99.52 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 1.61 61.17 99.9 0.075 0.082 0.033 0.998 12.1 6.2 39479
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 1.61 1.65 99.9 1.404 1.567 0.684 0.488 5.2 2841
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 1.61 61.17 37453 1962 99.87 0.2122 0.2106 0.2258 0.2436 0.26 RANDOM 32.174
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] -0.39 1.23 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.36 r_dihedral_angle_4_deg 15.582 r_dihedral_angle_3_deg 14.77 r_dihedral_angle_1_deg 7.239 r_mcangle_it 3.884 r_mcbond_other 2.355 r_mcbond_it 2.343 r_angle_refined_deg 1.532 r_angle_other_deg 1.354 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.36 r_dihedral_angle_4_deg 15.582 r_dihedral_angle_3_deg 14.77 r_dihedral_angle_1_deg 7.239 r_mcangle_it 3.884 r_mcbond_other 2.355 r_mcbond_it 2.343 r_angle_refined_deg 1.532 r_angle_other_deg 1.354 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2335 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing