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Structure of 2S albumin seed protein from Dolichos
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 Sodium acetate trihydrate, Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 1.93 36.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.158 α = 90 b = 65.158 β = 90 c = 118.167 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.88560 ESRF BM14
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 1.28 31.41 97 0.054 0.067 0.039 0.986 15.6 2.8 140457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.294 0.432 0.341 0.866
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 3OYO 1.28 31.41 126208 14272 96.99 0.13262 0.12837 0.1295 0.1698 0.1606 RANDOM 12.296
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] -3.41 -3.41 6.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.226 r_dihedral_angle_4_deg 20.873 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 7.308 r_rigid_bond_restr 4.126 r_long_range_B_refined 3.241 r_scangle_other 3.095 r_long_range_B_other 3.069 r_scbond_it 2.765 r_scbond_other 2.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.226 r_dihedral_angle_4_deg 20.873 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 7.308 r_rigid_bond_restr 4.126 r_long_range_B_refined 3.241 r_scangle_other 3.095 r_long_range_B_other 3.069 r_scbond_it 2.765 r_scbond_other 2.756 r_mcangle_it 2.37 r_mcangle_other 2.37 r_angle_refined_deg 2.169 r_mcbond_it 2.055 r_mcbond_other 2.032 r_angle_other_deg 1.628 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.015 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5247 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing