4EMF | pdb_00004emf

Crystal structure of the complex of type I Ribosome inactivating protein in complex with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.77 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.87	α = 90
b = 129.87	β = 90
c = 39.78	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	2010-10-21	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 Merge 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	1.77	64.93	99.9	0.063	13.2		23026	23026

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.87	99.6		0.565	2.4

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	3S9Q	1.77	33	23026	23026	1238	99.93	0.17453	0.1712	0.1682	0.1693	0.22772	0.2234	RANDOM	30.163

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]
-1.83	-0.91		-1.83		2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.677
r_dihedral_angle_4_deg	18.523
r_dihedral_angle_3_deg	13.514
r_dihedral_angle_1_deg	5.733
r_scangle_it	5.195
r_scbond_it	3.449
r_mcangle_it	2.131
r_angle_refined_deg	2.064
r_mcbond_it	1.268
r_chiral_restr	0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.677
r_dihedral_angle_4_deg	18.523
r_dihedral_angle_3_deg	13.514
r_dihedral_angle_1_deg	5.733
r_scangle_it	5.195
r_scbond_it	3.449
r_mcangle_it	2.131
r_angle_refined_deg	2.064
r_mcbond_it	1.268
r_chiral_restr	0.144
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	55

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.