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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 9RI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein solution (100 mg/ml):
40 mM Tris, pH 7.4, 2 mM MgCl2
Well solution:
0.15 M DL-malic acid, pH 7.0, 20 % PEG 3350
Drops: 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.26 α = 90 b = 53.42 β = 96.093 c = 49.02 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD MARMOSAIC 225 mm CCD 2013-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97372 ESRF ID29
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 1.3 24.53 88.1 0.037 0.052 0.036 0.998 14.8 2.9 39795
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) 1.3 1.33 37.3 0.502 0.71 0.502 0.433 1.4 1.6
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 1.305 24.53 39783 1982 87.808 0.15 0.1475 0.1424 0.189 0.1816 20.116
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] -0.278 -0.037 -0.29 0.563
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.833 r_dihedral_angle_6_deg 15.952 r_lrange_other 15.389 r_dihedral_angle_3_deg 13.016 r_scangle_it 10.932 r_scangle_other 10.927 r_mcangle_other 9.039 r_mcangle_it 9.037 r_scbond_it 7.837 r_scbond_other 7.836
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.833 r_dihedral_angle_6_deg 15.952 r_lrange_other 15.389 r_dihedral_angle_3_deg 13.016 r_scangle_it 10.932 r_scangle_other 10.927 r_mcangle_other 9.039 r_mcangle_it 9.037 r_scbond_it 7.837 r_scbond_other 7.836 r_dihedral_angle_1_deg 6.707 r_mcbond_it 6.534 r_mcbond_other 6.504 r_dihedral_angle_2_deg 5.975 r_rigid_bond_restr 4.706 r_angle_refined_deg 2.093 r_angle_other_deg 0.701 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.178 r_nbd_other 0.173 r_symmetry_nbd_refined 0.142 r_chiral_restr 0.104 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1478 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement