3N31

Crystal Structure of the complex of type I ribosome inactivating protein with fucose at 2.1A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.153	α = 90
b = 129.153	β = 90
c = 39.366	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MAR CCD 165 mm	mirror	2008-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8148	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	64.58	97.3	0.05	14.2		14192	14192			35.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22	92.4		0.175	4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1AHA	2.11	64.58	14192	13134	703	97.53	0.17847	0.17638	0.17395	0.22627	RANDOM	33.838

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]
-2.5	-1.25		-2.5		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.701
r_dihedral_angle_4_deg	20.085
r_dihedral_angle_3_deg	15.696
r_dihedral_angle_1_deg	6.255
r_scangle_it	5.693
r_scbond_it	3.712
r_angle_refined_deg	2.228
r_mcangle_it	2.132
r_mcbond_it	1.247
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.701
r_dihedral_angle_4_deg	20.085
r_dihedral_angle_3_deg	15.696
r_dihedral_angle_1_deg	6.255
r_scangle_it	5.693
r_scbond_it	3.712
r_angle_refined_deg	2.228
r_mcangle_it	2.132
r_mcbond_it	1.247
r_chiral_restr	0.136
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	45

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.