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Crystal structure of the Vitronectin hemopexin-like domain binding Sodium-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 UL PROTEIN SOLUTION + 1 UL
PRECIPITATE SOLUTION containing 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM
NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE,
11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D-
(+)-TREHALOSE. Crystals were soaked with 1 mM EDTA, 5 mM SODIUM SULFATE, 27 mM SODIUM NITRATE, 20 mM BisTris pH 7.0, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D-(+)-TREHALOSE.
Crystal Properties Matthews coefficient Solvent content 1.92 35.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.582 α = 90 b = 124.905 β = 119.5 c = 40.778 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 PIXEL DECTRIS PILATUS 6M 2020-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 35.52 97.6 0.07 9.9 3.5 23279
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 94.8 0.612 2 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7txr 2 35.52 21837 1419 97.45 0.1878 0.1842 0.1914 0.247 0.2479 RANDOM 32.55
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] -0.06 0.03 0.12 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.752 r_dihedral_angle_4_deg 18 r_dihedral_angle_3_deg 15.012 r_dihedral_angle_1_deg 7.416 r_angle_refined_deg 1.393 r_angle_other_deg 1.207 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.752 r_dihedral_angle_4_deg 18 r_dihedral_angle_3_deg 15.012 r_dihedral_angle_1_deg 7.416 r_angle_refined_deg 1.393 r_angle_other_deg 1.207 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3123 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing