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Human afamin orthorhombic crystal form by controlled hydration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30 % PEG 1000, 270 mM CH3COONH4, 3% 6-aminohexanoic acid (ACA). 1.5 uL 5 mg/mL Stock + 1.5 uL precipitant. Streak seeding followed by micro-seeding immediately after pipetting with no pre-equilibration of the drop. Controlled hydration experiment for data collection.
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.773 α = 90 b = 113.325 β = 90 c = 48.796 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 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 1.9 78.85 98.9 0.049 0.058 0.03 0.999 14.9 3.55 48102 33.4
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 1.9 1.94 95.8 0.868 1.031 0.547 0.728 2 3.36
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 2VUE 1.9 78.85 45558 2460 98.57 0.17905 0.17686 0.1878 0.219 0.2273 RANDOM 44.477
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] -1.31 -1.37 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 16.421 r_long_range_B_refined 9.543 r_long_range_B_other 9.531 r_scangle_other 6.464 r_dihedral_angle_1_deg 5.898 r_mcangle_it 4.615 r_mcangle_other 4.615 r_scbond_it 4.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 16.421 r_long_range_B_refined 9.543 r_long_range_B_other 9.531 r_scangle_other 6.464 r_dihedral_angle_1_deg 5.898 r_mcangle_it 4.615 r_mcangle_other 4.615 r_scbond_it 4.228 r_scbond_other 4.212 r_mcbond_it 2.887 r_mcbond_other 2.886 r_angle_refined_deg 1.611 r_angle_other_deg 1.041 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4637 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement autoPROC data collection EDNA data collection XSCALE data scaling pointless data scaling BALBES phasing ARP/wARP model building XDS data reduction