Experiment: 5EJB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B9B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	100mM sodium acetate pH 5.0, 1.75M lithium sulfate, 100mM magnesium sulfate, 3.4 % isopropanol

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.61	α = 90
b = 163.5	β = 94.13
c = 147.94	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 315r		2014-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.99969	ALS	8.2.2

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	3.2	49.62	99.63	0.122	8.37	3.99		80411

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	3.2	3.28	99.6		0.666	1.9	4.07

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2B9B	3.2	49.62	80411	4233	99.63	0.2542	0.2527	0.2833	RANDOM	95.232

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]
2.43		2.35	2.39		-5.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.769
r_dihedral_angle_3_deg	20.092
r_dihedral_angle_4_deg	15.765
r_dihedral_angle_1_deg	6.757
r_mcangle_it	5.097
r_scbond_it	4.091
r_mcbond_it	3.028
r_angle_refined_deg	1.541
r_chiral_restr	0.099
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.769
r_dihedral_angle_3_deg	20.092
r_dihedral_angle_4_deg	15.765
r_dihedral_angle_1_deg	6.757
r_mcangle_it	5.097
r_scbond_it	4.091
r_mcbond_it	3.028
r_angle_refined_deg	1.541
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20133
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	282

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
MOLREP	phasing
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 R01GM133198.