9TPF | pdb_00009tpf

The structure of the orthorhombic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M2T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	The crystal was grown at 4 degrees C in PACT condition B12 (0.01 M zinc chloride, 0.1 M MES pH 6, 20 % PEG 6000).

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.589	α = 90
b = 95.47	β = 90
c = 96.339	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	100	PIXEL	DECTRIS PILATUS 6M		2015-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.77	67.8	99.7	0.106	0.11	0.999	14.8	13.3		72825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.81	99.3		2.552	2.661	0.629	1	12.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	47.735	69469	3452	99.97	0.1823	0.1922	0.2333	0.2467	39.79

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]
0.974573188			-16.04594		15.0713668

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	13.8854
s_dihedral_angle_3_deg	10.7443
s_dihedral_angle_1_deg	6.9966
s_dihedral_angle_2_deg	4.5435
s_angle_nonh_deg	2.0041
s_hbond_nbd	0.2465
s_nbd	0.2308
s_nbtor	0.2244
s_symmetry_nbd	0.1782
s_symmetry_hbond_nbd	0.1734

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	13.8854
s_dihedral_angle_3_deg	10.7443
s_dihedral_angle_1_deg	6.9966
s_dihedral_angle_2_deg	4.5435
s_angle_nonh_deg	2.0041
s_hbond_nbd	0.2465
s_nbd	0.2308
s_nbtor	0.2244
s_symmetry_nbd	0.1782
s_symmetry_hbond_nbd	0.1734
s_metal_ion	0.1143
s_chiral_restr	0.0871
s_bond_nonh_d	0.0121
s_planes	0.0093

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3919
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	118

Software

Software
Software Name	Purpose
Servalcat	refinement
iMOSFLM	data reduction
SCALA	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.