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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:
1.92 ammonium suplhate, 0.096 M Bis-Tris, pH 5.5
Drop: 300 nl (protein) + 150 nl (well solution)
Cryo: 250 nl of 40% glycerol were added to the drop.
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.55 α = 90 b = 78.55 β = 90 c = 70.48 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 2022-02-27 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 1.6 24.88 99.9 0.146 0.163 0.071 0.994 8.1 9.5 29652
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) 1.6 1.63 99.8 1.148 1.384 0.761 0.825 1.3 5.7
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 1.6 24.88 29652 1489 99.822 0.198 0.195 0.196 0.2478 0.248 28.275
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] 2.516 2.516 -5.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.058 r_dihedral_angle_3_deg 13.779 r_lrange_it 6.809 r_lrange_other 6.691 r_dihedral_angle_1_deg 6.623 r_dihedral_angle_2_deg 5.407 r_scangle_it 4.052 r_scangle_other 3.973 r_scbond_it 2.698 r_scbond_other 2.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.058 r_dihedral_angle_3_deg 13.779 r_lrange_it 6.809 r_lrange_other 6.691 r_dihedral_angle_1_deg 6.623 r_dihedral_angle_2_deg 5.407 r_scangle_it 4.052 r_scangle_other 3.973 r_scbond_it 2.698 r_scbond_other 2.646 r_angle_refined_deg 2.265 r_mcangle_it 1.988 r_mcangle_other 1.987 r_mcbond_it 1.421 r_mcbond_other 1.42 r_angle_other_deg 0.813 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.133 r_nbd_other 0.104 r_symmetry_nbd_refined 0.095 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 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 222 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement