8OFD | pdb_00008ofd

Crystal structure of beta-conglutin from Lupinus albus refined to 2.81 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	281	40% (v/v) Tacsimate pH 7.0, 50 mM HEPES pH 7.0, 2 mM Spermine, and 2 mM Hexaamine cobalt (III)

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.63	α = 90
b = 166.63	β = 90
c = 40.098	γ = 120

Symmetry
Space Group	P 3 2 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	RIGAKU HyPix-6000HE		2022-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54184

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	2.81	21.77	99.7	0.17	0.182	0.064	0.993	9.1	7.8		15700			55

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.81	2.96	100		1.001	1.067	0.366	0.657	2	8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.81	21.767	15686	774	99.771	0.208	0.204	0.23	0.2772	0.31	62.202

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]
0.895			0.895		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.804
r_dihedral_angle_6_deg	14.932
r_lrange_other	12.243
r_lrange_it	12.238
r_dihedral_angle_2_deg	11.377
r_dihedral_angle_1_deg	8.748
r_scangle_it	7.904
r_scangle_other	7.903
r_mcangle_it	7.673
r_mcangle_other	7.672
r_scbond_it	5.08
r_scbond_other	5.079
r_mcbond_it	4.955
r_mcbond_other	4.941
r_angle_refined_deg	1.317
r_angle_other_deg	0.439
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_other	0.242
r_nbd_refined	0.228
r_symmetry_nbd_refined	0.221
r_symmetry_nbd_other	0.218
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_other	0.159
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.051
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3281
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing