3NJS | pdb_00003njs

Crystal structure of the complex formed between typeI ribosome inactivating protein and lactose at 2.1A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.44	α = 90
b = 130.44	β = 90
c = 38.473	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	mirror	2010-05-13	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	2.1	65.2	99.1	0.07	26		13390	13390			35.2

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	2.1	2.14	95.1		0.433	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1AHA	2.1	37.65	13390	13390	706	99.12	0.22631	0.22564	0.22382	0.25	0.26073	0.28	RANDOM	54.385

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]
-4.21	-2.1		-4.21		6.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.631
r_dihedral_angle_4_deg	19.544
r_dihedral_angle_3_deg	14.921
r_scangle_it	2.606
r_dihedral_angle_1_deg	1.654
r_angle_refined_deg	1.627
r_scbond_it	1.61
r_mcangle_it	1.59
r_mcbond_it	0.886
r_symmetry_vdw_refined	0.363

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.631
r_dihedral_angle_4_deg	19.544
r_dihedral_angle_3_deg	14.921
r_scangle_it	2.606
r_dihedral_angle_1_deg	1.654
r_angle_refined_deg	1.627
r_scbond_it	1.61
r_mcangle_it	1.59
r_mcbond_it	0.886
r_symmetry_vdw_refined	0.363
r_nbtor_refined	0.334
r_symmetry_hbond_refined	0.306
r_nbd_refined	0.257
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	57

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.