7U1H | pdb_00007u1h

Crystal structure of Lens culinaris vicilin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.01 M Zinc Chloride, 0.1 M Sodium acetate trihydrate, 15% PEG6000, with 20% glycerol as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.441	α = 90
b = 92.504	β = 90
c = 143.738	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-08-18	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	2.5	143.74	98.6	0.144	0.172	0.093	0.991	9.6	6.2		39945

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	2.5	2.6			0.782	0.939	0.513	0.812		6.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1UIK	2.5	77.909	39887	2073	98.239	0.204	0.1992	0.2	0.2839	0.28	36.052

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]
5.473			-2.584		-2.889

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.872
r_dihedral_angle_3_deg	19.473
r_dihedral_angle_4_deg	19.33
r_dihedral_angle_1_deg	8.321
r_lrange_it	7.777
r_lrange_other	7.777
r_scangle_it	5.272
r_scangle_other	5.272
r_mcangle_it	4.539
r_mcangle_other	4.539
r_scbond_it	3.249
r_scbond_other	3.248
r_mcbond_it	2.874
r_mcbond_other	2.874
r_angle_refined_deg	1.677
r_angle_other_deg	1.204
r_symmetry_xyhbond_nbd_refined	0.23
r_symmetry_nbd_refined	0.229
r_nbd_other	0.226
r_nbd_refined	0.215
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_other	0.131
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8688
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms

Software

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