1TFM | pdb_00001tfm

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	NaCl,Ammonium Sulphate, Dioxane, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.7	73.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.422	α = 90
b = 109.422	β = 90
c = 309.798	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	IMAGE PLATE	MARRESEARCH	mirrors	2001-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8453	EMBL/DESY, HAMBURG	X11

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	2.8	20	95.8	0.057	33.5	42.8		26570			91

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	2.8	2.85			0.433	2		1333

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1pc8	2.8	20	26570	1301	100	0.23998	0.23433	0.28856	RANDOM	58.406

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]
5.43	2.72		5.43		-8.15

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	10.549
r_dihedral_angle_1_deg	10.107
r_scbond_it	7.449
r_mcangle_it	3.951
r_mcbond_it	2.272
r_angle_refined_deg	1.716
r_symmetry_hbond_refined	0.558
r_nbd_refined	0.32
r_chiral_restr	0.3
r_xyhbond_nbd_refined	0.269

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	10.549
r_dihedral_angle_1_deg	10.107
r_scbond_it	7.449
r_mcangle_it	3.951
r_mcbond_it	2.272
r_angle_refined_deg	1.716
r_symmetry_hbond_refined	0.558
r_nbd_refined	0.32
r_chiral_restr	0.3
r_xyhbond_nbd_refined	0.269
r_symmetry_vdw_refined	0.265
r_gen_planes_refined	0.023
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3813
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	182

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.