7U1I

Crystal structure of Pisum sativum vicilin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.075M Sodium fluoride, 0.1M Bis-tris propane, 10% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.316	α = 90
b = 52.688	β = 95.193
c = 127.844	γ = 90

Symmetry
Space Group	P 1 21 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	DECTRIS PILATUS3 S 6M		2021-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.98	CLSI	08B1-1

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	3.1	98.104	85.9	0.102	0.142	0.099	0.985	6	3		20422

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	3.1	3.31			0.288	0.401	0.278	0.878		2.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1UIK	3.1	98.104	20413	1022	84.386	0.19	0.1847	0.285	46.421

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]
-2.951		-2.324	1.555		1.788

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.457
r_dihedral_angle_3_deg	21.108
r_dihedral_angle_4_deg	19.876
r_dihedral_angle_1_deg	8.17
r_lrange_it	7.734
r_lrange_other	7.734
r_mcangle_it	4.982
r_mcangle_other	4.981
r_scangle_it	4.809
r_scangle_other	4.809
r_mcbond_it	3.049
r_mcbond_other	3.049
r_scbond_it	2.862
r_scbond_other	2.862
r_angle_refined_deg	1.487
r_angle_other_deg	1.113
r_nbd_other	0.267
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.165
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.051
r_bond_refined_d	0.006
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	8488
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
DIALS	data reduction
DIALS	data scaling