3NX9

Crystal structure of type I ribosome inactivating protein in complex with maltose at 1.7A resolution

X-RAY DIFFRACTION

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
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.955	α = 90
b = 129.955	β = 90
c = 40.156	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	MARRESEARCH	mirror	2010-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.7	37.8	96.7	0.062	33.8		27861	27861			22.2

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	1.7	1.73	80.6		0.282	3.3

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	1.7	37.8	25578	25578	1359	96.7	0.1829	0.18214	0.17992	0.2246	RANDOM	27.814

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]
-1.25	-0.62		-1.25		1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.346
r_dihedral_angle_4_deg	16.147
r_dihedral_angle_3_deg	11.107
r_dihedral_angle_1_deg	4.315
r_scangle_it	3.935
r_scbond_it	2.726
r_mcangle_it	1.573
r_angle_refined_deg	1.352
r_mcbond_it	1.047
r_symmetry_hbond_refined	0.604

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.346
r_dihedral_angle_4_deg	16.147
r_dihedral_angle_3_deg	11.107
r_dihedral_angle_1_deg	4.315
r_scangle_it	3.935
r_scbond_it	2.726
r_mcangle_it	1.573
r_angle_refined_deg	1.352
r_mcbond_it	1.047
r_symmetry_hbond_refined	0.604
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	57

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 R01GM133198.