5VF5 | pdb_00005vf5

Crystal structure of the vicilin from Solanum melongena, re-refinement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CAD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829850mM Tris-Cl, 1.5 M Sodium malonate, 10% Peg 3350
Crystal Properties
Matthews coefficientSolvent content
2.5651.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.33α = 90
b = 119.33β = 90
c = 158.19γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4922.7199.90.06120.511.870495
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.571000.4764.310.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5CAD1.4922.7166897355699.840.132150.130520.130.162630.16RANDOM19.839
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]
-0.55-0.27-0.551.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.38
r_dihedral_angle_4_deg17.566
r_dihedral_angle_3_deg12.83
r_sphericity_bonded11.256
r_dihedral_angle_1_deg6.402
r_rigid_bond_restr5.063
r_long_range_B_refined4.223
r_long_range_B_other4.222
r_scangle_other4.038
r_scbond_other3.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.38
r_dihedral_angle_4_deg17.566
r_dihedral_angle_3_deg12.83
r_sphericity_bonded11.256
r_dihedral_angle_1_deg6.402
r_rigid_bond_restr5.063
r_long_range_B_refined4.223
r_long_range_B_other4.222
r_scangle_other4.038
r_scbond_other3.538
r_scbond_it3.536
r_mcangle_it2.451
r_mcangle_other2.45
r_mcbond_it2.133
r_mcbond_other2.12
r_angle_refined_deg1.686
r_angle_other_deg1.52
r_chiral_restr0.121
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2948
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement