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Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium formate; 20% polyethylene glycol 3350 (wt/vol)
Crystal Properties Matthews coefficient Solvent content 2.55 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.977 α = 90 b = 69.231 β = 90 c = 137.828 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2021-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.99 ESRF ID30B
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 2.78 50.338 97.6 0.2 0.21 0.06 0.997 7.3 4.4 12325
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 2.78 2.93 1.6 0.9 0.9 0.15 0.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.87 50.338 12249 621 98.102 0.235 0.2327 0.5662 0.2805 0.6002 RANDOM 99.374
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] -3.939 3.333 0.606
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 25.863 r_scangle_it 19.849 r_dihedral_angle_3_deg 18.19 r_mcangle_it 16.577 r_dihedral_angle_6_deg 13.91 r_scbond_it 13.106 r_mcbond_it 10.8 r_dihedral_angle_1_deg 9.077 r_dihedral_angle_2_deg 7.037 r_angle_refined_deg 2.182
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 25.863 r_scangle_it 19.849 r_dihedral_angle_3_deg 18.19 r_mcangle_it 16.577 r_dihedral_angle_6_deg 13.91 r_scbond_it 13.106 r_mcbond_it 10.8 r_dihedral_angle_1_deg 9.077 r_dihedral_angle_2_deg 7.037 r_angle_refined_deg 2.182 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.309 r_nbd_refined 0.272 r_symmetry_xyhbond_nbd_refined 0.225 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.155 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2795 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing