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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 295 Protein solution (70 mg/ml):
40 mM Tris, pH 7.4, 2 mM MgCl2
Well solution:
2.4 M Sodium malonate pH 7.0
Drops: 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.37 α = 90 b = 80.37 β = 90 c = 70.16 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 CCD MARMOSAIC 225 mm CCD 2014-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97372 ESRF BM14
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 2.3 19.6 96.4 0.37 0.4 0.15 0.989 13.3 12.9 10321
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) 2.3 2.38 99.8 1.636 1.86 0.873 0.334 1.6 8.2
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 2.3 19.6 10319 474 96.493 0.178 0.1747 0.1707 0.2479 0.2485 26.873
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] 0.586 0.586 -1.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.66 r_dihedral_angle_6_deg 15.29 r_dihedral_angle_2_deg 12.08 r_dihedral_angle_1_deg 7.462 r_lrange_it 5.248 r_lrange_other 5.234 r_scangle_it 3.828 r_scangle_other 3.827 r_scbond_it 2.378 r_scbond_other 2.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.66 r_dihedral_angle_6_deg 15.29 r_dihedral_angle_2_deg 12.08 r_dihedral_angle_1_deg 7.462 r_lrange_it 5.248 r_lrange_other 5.234 r_scangle_it 3.828 r_scangle_other 3.827 r_scbond_it 2.378 r_scbond_other 2.376 r_angle_refined_deg 2.286 r_mcangle_it 2.063 r_mcangle_other 2.063 r_mcbond_it 1.297 r_mcbond_other 1.286 r_angle_other_deg 0.756 r_nbd_refined 0.225 r_symmetry_nbd_other 0.204 r_nbd_other 0.196 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.098 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling Aimless data scaling REFMAC refinement PHASER phasing