3S60 | pdb_00003s60

Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in free state obtained at 25 degree Celsius

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S5V	PDB ENTRY 3S5V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	2.0 M (NH4)SO4 and 0.1 M Tris-HCl (pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.467	α = 90
b = 40.658	β = 90
c = 70.374	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	298	CCD	RIGAKU SATURN 944+		2010-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	26.61	95	0.081	8.7	2.48	13272	13272	3	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	91.5		0.309	1.5	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3S5V	1.6	26.61	1	13272	13272	1490	94.98	0.18706	0.18242	0.19	0.22793	0.24	RANDOM	27.666

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]
-0.11			-0.38		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.559
r_dihedral_angle_3_deg	11.054
r_dihedral_angle_4_deg	8.582
r_scangle_it	8.06
r_scbond_it	6.624
r_dihedral_angle_1_deg	6.356
r_mcangle_it	5.634
r_mcbond_it	4.45
r_angle_refined_deg	1.933
r_chiral_restr	0.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.559
r_dihedral_angle_3_deg	11.054
r_dihedral_angle_4_deg	8.582
r_scangle_it	8.06
r_scbond_it	6.624
r_dihedral_angle_1_deg	6.356
r_mcangle_it	5.634
r_mcbond_it	4.45
r_angle_refined_deg	1.933
r_chiral_restr	0.162
r_bond_refined_d	0.022
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	983
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.