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Crystal structure of the Vitronectin hemopexin-like domain binding Calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 UL PROTEIN SOLUTION + 1 UL
PRECIPITATE SOLUTION contaning 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 the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES
Crystal Properties Matthews coefficient Solvent content 1.95 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.832 α = 90 b = 125.575 β = 119.25 c = 40.883 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 2020-09-12 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 1.7 35.69 97.9 0.061 10.6 3.5 38571
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 1.7 1.73 0.593
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 6O5E 1.7 35.69 36276 2261 97.85 0.173 0.1705 0.1811 0.2102 0.2154 RANDOM 23.966
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] 0.3 -0.36 0.49 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.982 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 7.598 r_angle_refined_deg 1.546 r_angle_other_deg 1.37 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.982 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 7.598 r_angle_refined_deg 1.546 r_angle_other_deg 1.37 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing