Experiment: 2E59

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E56	PDB ENTRY 2E56

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	277	15% PEG3350, 40mM Na-citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.795	α = 90
b = 52.795	β = 90
c = 110.889	γ = 90

Symmetry
Space Group	P 41 21 2

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	RIGAKU JUPITER 210		2006-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	27.72	90.7	0.1	9.6	11.2		7629			25.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2E56	2.21	27.72	2.5	6291	297	78.88	0.20842	0.20583	0.26326	RANDOM	37.455

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]
1.08			1.08		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_3_deg	16.278
r_dihedral_angle_4_deg	8.002
r_dihedral_angle_1_deg	6.597
r_scangle_it	6.181
r_mcangle_it	6.072
r_scbond_it	4.389
r_mcbond_it	4.014
r_angle_refined_deg	1.495
r_nbtor_refined	0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_3_deg	16.278
r_dihedral_angle_4_deg	8.002
r_dihedral_angle_1_deg	6.597
r_scangle_it	6.181
r_mcangle_it	6.072
r_scbond_it	4.389
r_mcbond_it	4.014
r_angle_refined_deg	1.495
r_nbtor_refined	0.344
r_nbd_refined	0.259
r_symmetry_vdw_refined	0.255
r_xyhbond_nbd_refined	0.233
r_symmetry_hbond_refined	0.218
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1162
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	123

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.