Experiment: 3EMB

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	10mM AdoMet, 1mM 7MeGpppG, 18% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.236	α = 90
b = 61.297	β = 90
c = 128.012	γ = 90

Symmetry
Space Group	P 21 21 21

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	mirrors	2007-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.3	64.02	100	0.137	11.4	5.8	14380	13695

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)
	2.3	2.42	100		0.539	3	5.1	2035

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ELU	2.3	35.03	13614	12966	677	99.98	0.16921	0.16921	0.16616	0.22884	RANDOM	19.356

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]
-0.2			-0.05		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.139
r_dihedral_angle_4_deg	16.691
r_dihedral_angle_3_deg	16.037
r_scangle_it	7.774
r_dihedral_angle_1_deg	5.762
r_scbond_it	4.942
r_mcangle_it	3.029
r_mcbond_it	1.781
r_angle_refined_deg	1.549
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.139
r_dihedral_angle_4_deg	16.691
r_dihedral_angle_3_deg	16.037
r_scangle_it	7.774
r_dihedral_angle_1_deg	5.762
r_scbond_it	4.942
r_mcangle_it	3.029
r_mcbond_it	1.781
r_angle_refined_deg	1.549
r_nbtor_refined	0.295
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.124
r_xyhbond_nbd_refined	0.12
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2088
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	89

Software

Software
Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
REFMAC	refinement
SCALA	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.