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Structure of vicilin from Capsicum annuum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 50mM HEPES, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.03 α = 90 b = 148.03 β = 90 c = 148.03 γ = 90
Symmetry Space Group P 21 3
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 2016-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9787 ESRF BM14
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 2.16 50 100 0.11 10.5 6.2 55184
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 2.16 2.28 100 0.622 2.7 6.1
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 5CAD 2.16 50 54852 2983 99.96 0.17735 0.17515 0.1835 0.21671 0.2191 RANDOM 37.354
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_4_deg 20.31 r_dihedral_angle_3_deg 14.669 r_long_range_B_other 8.164 r_long_range_B_refined 8.162 r_dihedral_angle_1_deg 6.743 r_scangle_other 6.473 r_scbond_it 4.217 r_scbond_other 4.212 r_mcangle_it 4.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_4_deg 20.31 r_dihedral_angle_3_deg 14.669 r_long_range_B_other 8.164 r_long_range_B_refined 8.162 r_dihedral_angle_1_deg 6.743 r_scangle_other 6.473 r_scbond_it 4.217 r_scbond_other 4.212 r_mcangle_it 4.155 r_mcangle_other 4.154 r_mcbond_it 2.987 r_mcbond_other 2.987 r_angle_refined_deg 1.805 r_angle_other_deg 1.02 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 5808 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing Coot model building