6V7L | pdb_00006v7l

The structure of the P212121 crystal form of canavalin at 173 K

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Crystals were grown by sitting drop vapor diffusion from 18% PEG 3350 in 0.1 M HEPES reservoirs. The drops were equal amounts of a 40 mg/ml solution of precanavalin (not treated with any exogenous protease) in water. Crystals grew only after six to eight weeks at room temperature.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.889	α = 90
b = 90.511	β = 90
c = 183.739	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	173	PIXEL	DECTRIS PILATUS3 R CdTe 300K		2018-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.75	60	73.4	0.282	0.275	0.29	0.07	0.998	9.9	17.2		28813			54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85	8.8		0.025	0.4	2.3

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1CAX	2.8	30	27012	1442	78.86	0.1962	0.1933	0.252	RANDOM	78.346

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]
-1.59			-1.34		2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.978
r_dihedral_angle_4_deg	18.191
r_dihedral_angle_3_deg	16.143
r_dihedral_angle_1_deg	7.424
r_angle_refined_deg	1.285
r_angle_other_deg	1.128
r_chiral_restr	0.042
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.978
r_dihedral_angle_4_deg	18.191
r_dihedral_angle_3_deg	16.143
r_dihedral_angle_1_deg	7.424
r_angle_refined_deg	1.285
r_angle_other_deg	1.128
r_chiral_restr	0.042
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8406
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.