Experiment: 2EG5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EFJ	PDB ENTRY 2EFJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	25% PEG 3350, 200mM Li2SO4, 100mM Tris-HCl, 1mM SAH, 1mM xanthosine, 2mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.59	α = 90
b = 119.8	β = 102.16
c = 116.4	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	CCD	ADSC QUANTUM 4		2005-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4

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	2.2	30	95.2	0.079	13.1		75624	74901

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	2.2	2.3	93.4		0.443	3		10071

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	PDB ENTRY 2EFJ	2.2	30	71794	3830	96.68	0.233	0.23	0.23	0.284	0.28	RANDOM	44.845

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]
-0.83		0.42	-1.88		2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.845
r_dihedral_angle_3_deg	19.096
r_dihedral_angle_4_deg	12.874
r_dihedral_angle_1_deg	6.826
r_scangle_it	3.162
r_scbond_it	2.093
r_angle_refined_deg	1.734
r_mcangle_it	1.519
r_mcbond_it	0.897
r_symmetry_vdw_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.845
r_dihedral_angle_3_deg	19.096
r_dihedral_angle_4_deg	12.874
r_dihedral_angle_1_deg	6.826
r_scangle_it	3.162
r_scbond_it	2.093
r_angle_refined_deg	1.734
r_mcangle_it	1.519
r_mcbond_it	0.897
r_symmetry_vdw_refined	0.316
r_nbtor_refined	0.313
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.114
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10668
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	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.