5CIX

Structure of the complex of type 1 Ribosome inactivating protein with triethanolamine at 1.88 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.262	α = 90
b = 130.262	β = 90
c = 38.158	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		2015-02-15	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	1.88	32.57	99.5	0.074	0.0185	2.1		19516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	96.6		0.335	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JTP	1.88	32.57	17828	952	95.64	0.1686	0.166	0.2178	RANDOM	44.053

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]
0.04	0.02		0.04		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_4_deg	18.393
r_dihedral_angle_3_deg	13.24
r_dihedral_angle_1_deg	5.81
r_mcangle_it	4.511
r_mcbond_other	3.444
r_mcbond_it	3.442
r_angle_refined_deg	1.794
r_angle_other_deg	0.887
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_4_deg	18.393
r_dihedral_angle_3_deg	13.24
r_dihedral_angle_1_deg	5.81
r_mcangle_it	4.511
r_mcbond_other	3.444
r_mcbond_it	3.442
r_angle_refined_deg	1.794
r_angle_other_deg	0.887
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1910
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	model building
PDB_EXTRACT	data extraction
SCALEPACK	data reduction
Coot	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.