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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 (55 mg/ml):
40 mM Tris, pH 7.4, 2 mM MgCl2
Well solution:
0.1 M succinic acid, pH 7.0, 15 % PEG 3350
Drops: 2:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.01 38.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.03 α = 90 b = 53.76 β = 100.62 c = 44.65 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 100 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 1.6 19.19 94.6 0.046 0.064 0.046 0.999 13.2 3.1 21566
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 80 1.004 1.419 1.004 0.415 1 3
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 19.19 21566 1084 94.472 0.163 0.1608 0.1534 0.2002 0.1887 21.839
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] -0.068 -0.089 -1.242 1.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.891 r_dihedral_angle_3_deg 12.619 r_dihedral_angle_2_deg 7.912 r_dihedral_angle_1_deg 6.902 r_lrange_it 5.589 r_lrange_other 5.418 r_scangle_it 3.633 r_scangle_other 3.631 r_scbond_it 2.83 r_scbond_other 2.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.891 r_dihedral_angle_3_deg 12.619 r_dihedral_angle_2_deg 7.912 r_dihedral_angle_1_deg 6.902 r_lrange_it 5.589 r_lrange_other 5.418 r_scangle_it 3.633 r_scangle_other 3.631 r_scbond_it 2.83 r_scbond_other 2.829 r_angle_refined_deg 2.27 r_mcangle_it 1.986 r_mcangle_other 1.986 r_mcbond_it 1.336 r_mcbond_other 1.326 r_angle_other_deg 0.76 r_xyhbond_nbd_refined 0.266 r_nbd_refined 0.218 r_nbd_other 0.199 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.154 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.085 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 1512 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 62
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement