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Human afamin monoclinic crystal form
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 6 293 1.5 uL PEG 1k 30%, CH3COONH4 180mM, 3% 6-aminohexanoic acid plus 1.5 uL 5 mg/ml protein stock 20mM HEPES ph7.5 150 mM NaCl, microseeding
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.915 α = 90 b = 112.872 β = 93.39 c = 109.228 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 2M Focussing Monochromator 2016-04-08 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) R Sym I (Observed) 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 2.08 109.04 89.6 0.044 0.038 0.99 13.59 2.9 66261 50.3
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 2.08 2.21 78.8 0.685 0.702 1.67 2.8
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 2.09 109.04 62919 3296 90.8 0.201 0.199 0.2072 0.237 0.2415 RANDOM 61.13
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] 1.97 -0.06 -2.09 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_4_deg 15.865 r_dihedral_angle_3_deg 15.744 r_long_range_B_refined 9.693 r_long_range_B_other 9.688 r_scangle_other 7.522 r_dihedral_angle_1_deg 6.138 r_mcangle_other 5.579 r_mcangle_it 5.578 r_scbond_it 4.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_4_deg 15.865 r_dihedral_angle_3_deg 15.744 r_long_range_B_refined 9.693 r_long_range_B_other 9.688 r_scangle_other 7.522 r_dihedral_angle_1_deg 6.138 r_mcangle_other 5.579 r_mcangle_it 5.578 r_scbond_it 4.784 r_scbond_other 4.784 r_mcbond_it 3.761 r_mcbond_other 3.76 r_angle_refined_deg 1.332 r_angle_other_deg 0.972 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 8994 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing