5VF5

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

X-RAY DIFFRACTION

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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	8	298	50mM Tris-Cl, 1.5 M Sodium malonate, 10% Peg 3350

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.33	α = 90
b = 119.33	β = 90
c = 158.19	γ = 120

Symmetry
Space Group	H 3 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	CCD	MARMOSAIC 225 mm CCD		2011-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95372	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	1.49	22.71	99.9	0.061	20.5	11.8		70495

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	1.49	1.57	100		0.476	4.3	10.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5CAD	1.49	22.71	66897	3556	99.84	0.13215	0.13052	0.16263	RANDOM	19.839

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		-0.55		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.38
r_dihedral_angle_4_deg	17.566
r_dihedral_angle_3_deg	12.83
r_sphericity_bonded	11.256
r_dihedral_angle_1_deg	6.402
r_rigid_bond_restr	5.063
r_long_range_B_refined	4.223
r_long_range_B_other	4.222
r_scangle_other	4.038
r_scbond_other	3.538
r_scbond_it	3.536
r_mcangle_it	2.451
r_mcangle_other	2.45
r_mcbond_it	2.133
r_mcbond_other	2.12
r_angle_refined_deg	1.686
r_angle_other_deg	1.52
r_chiral_restr	0.121
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003
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 Atoms	Number
Protein Atoms	2948
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement