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Integrin alpha(2) I-domain mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein solution (16.5 mg/ml):
40 mM Tris-HCl (pH 7.4), 2 mM MgCl2
Well solution:
1 M tri-Na citrate, 0.1 M Na cacodylate
Drop: 200 nl (protein) + 200 nl (well solution)
Cryo: 250 nl of 40% glycerol were added to the drop.
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.85 α = 90 b = 79.85 β = 90 c = 70.36 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS PILATUS 6M 2022-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
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 1.9 19.6 98.8 0.11 0.129 0.064 0.997 11.9 6.4 18155
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) 1.9 1.94 99.4 1.561 1.846 0.946 0.557 1.3 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 19.6 18155 886 98.199 0.163 0.1604 0.1589 0.2133 0.2121 37.402
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] 1.411 1.411 -2.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.721 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_2_deg 10.049 r_lrange_it 7.736 r_lrange_other 7.672 r_dihedral_angle_1_deg 7.062 r_scangle_it 6.083 r_scangle_other 6.081 r_scbond_other 4.32 r_scbond_it 4.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.721 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_2_deg 10.049 r_lrange_it 7.736 r_lrange_other 7.672 r_dihedral_angle_1_deg 7.062 r_scangle_it 6.083 r_scangle_other 6.081 r_scbond_other 4.32 r_scbond_it 4.316 r_mcangle_it 3.327 r_mcangle_other 3.326 r_mcbond_it 2.753 r_mcbond_other 2.752 r_angle_refined_deg 2.412 r_angle_other_deg 0.761 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.192 r_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.138 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.097 r_xyhbond_nbd_other 0.038 r_symmetry_nbd_refined 0.023 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 19
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement