9TPE | pdb_00009tpe

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

X-RAY DIFFRACTION

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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	8	293	The protein was concentrated to 4 mg/ml and a crystal was obtained after 24 weeks at room temperature in condition D10 of the PACT Premier screen (0.2 M magnesium chloride, 0.1 M Tris pH 8, 20 % PEG 6000). The crystal was cryoprotected with a 1:4 ratio of PEG 400 to well solution.

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.738	α = 90
b = 94.215	β = 96.44
c = 70.876	γ = 90

Symmetry
Space Group	P 1 21 1

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		2015-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9795	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	1.5	41.17	99.6	0.063	0.075	0.995	13.5	3.3		93826

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	1.5	1.53	96.3		0.141	0.179	0.956	5.6	2.4

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	1.5	29.711	96365	4810	98.96	0.1608	0.1606	0.2065	0.2058	18.06

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]
0.950830557		-1.28292229	5.03046504		-5.98129559

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	14.5452
s_dihedral_angle_3_deg	9.5464
s_dihedral_angle_1_deg	6.6451
s_dihedral_angle_2_deg	3.5461
s_angle_nonh_deg	2.0222
s_hbond_nbd	0.2618
s_nbd	0.241
s_symmetry_hbond_nbd	0.2369
s_nbtor	0.2259
s_symmetry_nbd	0.1864
s_chiral_restr	0.095
s_metal_ion	0.0597
s_bond_nonh_d	0.0132
s_planes	0.0102

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3919
Nucleic Acid Atoms
Solvent Atoms	807
Heterogen Atoms	94

Software

Software
Software Name	Purpose
Servalcat	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing