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Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OKL 5OKL_B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Stock: 5 mg/ml AFM in 20mM HEPES pH 7.5, 150mM NaCl, incubated with 10mM Gd-DO3A
Drop: 200 nL AFM stock + 200 nL of precipitate in hanging drop vapor diffusion (EMBL HTX)
Precipitant: 23 to 28% PEG4k, 0.2M NH4SO4, 0.1 M CH3COONH4, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.352 α = 90 b = 109.734 β = 90 c = 48.381 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS3 2M BE CRL 2018-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96598 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.69 75.24 85.2 0.18 0.2 0.99 5.6 4.7 9591 59.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 3.02 62 0.54 0.68 0.8 1.7 2.1
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 5OKL_B 2.69 75.24 9041 482 59.59 0.26629 0.26257 0.2674 0.33544 0.3442 RANDOM 56.545
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] -0.61 -0.67 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_3_deg 18.934 r_dihedral_angle_4_deg 11.986 r_long_range_B_refined 10.57 r_long_range_B_other 10.568 r_scangle_other 7.348 r_mcangle_it 6.902 r_mcangle_other 6.902 r_dihedral_angle_1_deg 5.599 r_scbond_it 4.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_3_deg 18.934 r_dihedral_angle_4_deg 11.986 r_long_range_B_refined 10.57 r_long_range_B_other 10.568 r_scangle_other 7.348 r_mcangle_it 6.902 r_mcangle_other 6.902 r_dihedral_angle_1_deg 5.599 r_scbond_it 4.315 r_scbond_other 4.314 r_mcbond_it 4.21 r_mcbond_other 4.209 r_angle_refined_deg 1.191 r_angle_other_deg 1.029 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3866 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling Aimless data scaling autoPROC data collection STARANISO data scaling PHASER phasing