7U1J | pdb_00007u1j

Crystal structure of Pisum sativum convicilin

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	6	293	0.15M Ammonium Acetate, 25% PEG3350, 0.05M Bis Tris

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 269.155	α = 90
b = 269.155	β = 90
c = 269.155	γ = 90

Symmetry
Space Group	F 2 3

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	2.7	134.941	99.8	0.127	0.151	0.081	0.995	8.9	5.5		44137

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	2.7	2.81			0.554	0.663	0.359	0.811		5.7

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	2.701	134.941	44134	2246	99.772	0.218	0.2149	0.22	0.281	0.28	43.743

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.477
r_dihedral_angle_3_deg	21.004
r_dihedral_angle_4_deg	20.163
r_lrange_it	9.667
r_lrange_other	9.666
r_dihedral_angle_1_deg	9.561
r_scangle_it	6.96
r_scangle_other	6.959
r_mcangle_it	6.28
r_mcangle_other	6.28
r_scbond_it	4.44
r_scbond_other	4.44
r_mcbond_it	4.096
r_mcbond_other	4.096
r_angle_refined_deg	1.768
r_angle_other_deg	1.223
r_nbd_refined	0.224
r_nbd_other	0.198
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_refined	0.183
r_symmetry_nbd_refined	0.171
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.068
r_xyhbond_nbd_other	0.045
r_bond_refined_d	0.009
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	8329
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

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