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Crystal structure of integrin a4b1 headpiece in complex with Bio-1211 (Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20% PEG-3350, 100 mM succinic acid
Crystal Properties Matthews coefficient Solvent content 2.63 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.46 α = 90 b = 109.64 β = 90 c = 131.19 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 PILATUS3 6M 2024-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97624 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.64 35.51 99.77 0.19 5.9 7.6 36481
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 2.64 2.84 0.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.64 35.508 1.33 35974 1808 98.66 0.2548 0.2528 0.2549 0.2903 0.2906
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.339 f_angle_d 0.512 f_chiral_restr 0.042 f_bond_d 0.004 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8036 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 326
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing