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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 1DZI
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: 200 nl of 40% glycerol were added to the drop.
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.22 α = 90 b = 79.22 β = 90 c = 70.41 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 RIGAKU HyPix-6000HE VariMax mirrors 2022-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541838
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 19.57 99.8 0.09 0.099 0.041 0.999 18.9 10.3 18175
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 1.94 100 0.693 0.797 0.389 0.845 3 7.8
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 19.57 18175 881 99.665 0.185 0.1817 0.1782 0.2424 0.2353 37.585
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] 1.535 1.535 -3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.69 r_dihedral_angle_3_deg 14.374 r_lrange_it 7.02 r_dihedral_angle_2_deg 6.935 r_lrange_other 6.853 r_dihedral_angle_1_deg 6.501 r_scangle_it 5.15 r_scangle_other 5.121 r_scbond_it 3.513 r_scbond_other 3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.69 r_dihedral_angle_3_deg 14.374 r_lrange_it 7.02 r_dihedral_angle_2_deg 6.935 r_lrange_other 6.853 r_dihedral_angle_1_deg 6.501 r_scangle_it 5.15 r_scangle_other 5.121 r_scbond_it 3.513 r_scbond_other 3.494 r_mcangle_other 3.053 r_mcangle_it 3.048 r_mcbond_it 2.317 r_mcbond_other 2.309 r_angle_refined_deg 2.047 r_angle_other_deg 0.68 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.182 r_symmetry_nbd_refined 0.1 r_nbd_other 0.098 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1503 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement