5Y42 | pdb_00005y42

Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2M lithium sulfate monohydrate, 0.1M Tris-Hcl, pH8.5, 30% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.226	α = 90
b = 171.226	β = 90
c = 75.85	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2015-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.9	85.61	100	0.198	0.996	12.6	12.2		28365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.648	2.1	11.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4HR6	2.9	85.01	26872	1438	99.87	0.20476	0.20209	0.21	0.25538	0.25	RANDOM	59.753

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]
-0.55	-0.28		-0.55		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.044
r_dihedral_angle_4_deg	15.308
r_dihedral_angle_3_deg	14.497
r_long_range_B_refined	11.45
r_long_range_B_other	11.45
r_dihedral_angle_1_deg	6.761
r_scangle_other	6.416
r_mcangle_it	6.272
r_mcangle_other	6.271
r_scbond_it	4.05
r_scbond_other	4.05
r_mcbond_it	3.971
r_mcbond_other	3.97
r_angle_refined_deg	1.691
r_angle_other_deg	1.077
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8009
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	15

Software

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