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Crystal structure of the Calf domains of Integrin Alpha5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M Bistris pH 5.5, 0.2M MgCl2, 25% PEG 3350 (wt/vol)
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.016 α = 90 b = 71.437 β = 90 c = 121.266 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 2M 2018-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.0 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.92 46.28 99.5 0.15 0.995 5.47 19.8 33875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.05 91 1.62 0.14 0.8
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 1.92 46.28 33797 1995 99.485 0.225 0.2218 0.2218 0.2822 0.2824 50.54
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] -3.034 3.139 -0.105
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 31.124 r_lrange_other 30.996 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_2_deg 16.935 r_dihedral_angle_6_deg 16.29 r_scangle_it 11.125 r_scangle_other 11.123 r_dihedral_angle_1_deg 10.222 r_mcangle_it 8.803 r_mcangle_other 8.802
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 31.124 r_lrange_other 30.996 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_2_deg 16.935 r_dihedral_angle_6_deg 16.29 r_scangle_it 11.125 r_scangle_other 11.123 r_dihedral_angle_1_deg 10.222 r_mcangle_it 8.803 r_mcangle_other 8.802 r_scbond_it 7.777 r_scbond_other 7.775 r_mcbond_it 6.424 r_mcbond_other 6.424 r_angle_refined_deg 1.944 r_angle_other_deg 0.757 r_symmetry_nbd_refined 0.278 r_xyhbond_nbd_refined 0.258 r_nbd_refined 0.223 r_nbd_other 0.209 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.123 r_chiral_restr 0.103 r_symmetry_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2528 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data scaling PHASER phasing