Experiment: 3LJB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Initial model derived from a low-resolution SeMet data set

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	300	5% PEG3350, 100 mM MES (pH 6.8), 100 mM MgCl2 and 0.01 mM Hexammine cobalt (III) chloride, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.147	α = 65.82
b = 57.366	β = 88.47
c = 57.491	γ = 74.87

Symmetry
Space Group	P 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	RAYONIX MX-225	Double crystal monochromator with 2 sets of mirrors	2008-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	100	97.1	0.103	0.062	14.91	3.52		21393		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	96.7		0.473	0.387	3.76	3.54	1547

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	Initial model derived from a low-resolution SeMet data set	2.4	19.95	20811	20309	1084	97.59	0.19634	0.19634	0.19314	0.21	0.25681	0.27	RANDOM	44.808

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]
0.23	0.02	0.55	-1.49	-0.84	1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.099
r_dihedral_angle_4_deg	19.647
r_dihedral_angle_3_deg	16.935
r_dihedral_angle_1_deg	4.921
r_scangle_it	2.803
r_scbond_it	1.665
r_mcangle_it	1.274
r_angle_refined_deg	1.152
r_angle_other_deg	0.881
r_mcbond_it	0.657

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.099
r_dihedral_angle_4_deg	19.647
r_dihedral_angle_3_deg	16.935
r_dihedral_angle_1_deg	4.921
r_scangle_it	2.803
r_scbond_it	1.665
r_mcangle_it	1.274
r_angle_refined_deg	1.152
r_angle_other_deg	0.881
r_mcbond_it	0.657
r_mcbond_other	0.104
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3639
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction

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.