Experiment: 5EJV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	1.0M Na Acetate/0.2M NaSCN/0.1M TRIS pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.139	α = 90
b = 63.139	β = 90
c = 160.441	γ = 90

Symmetry
Space Group	P 41

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	MARMOSAIC 225 mm CCD		2010-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.98	APS	31-ID

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	2.58	63.14	100	0.136	0.136	8.8	7.4		19787

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	2.58	2.72	100		0.912	0.912	0.8	7.4	2891

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	3L0L	2.58	63.14	18768	968	99.94	0.182	0.1793	0.2308	RANDOM	46.393

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]
0.11			0.11		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.671
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	18.181
r_dihedral_angle_1_deg	5.346
r_mcangle_it	4.133
r_mcbond_it	2.713
r_mcbond_other	2.709
r_angle_refined_deg	2.074
r_angle_other_deg	1.152
r_chiral_restr	0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.671
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	18.181
r_dihedral_angle_1_deg	5.346
r_mcangle_it	4.133
r_mcbond_it	2.713
r_mcbond_other	2.709
r_angle_refined_deg	2.074
r_angle_other_deg	1.152
r_chiral_restr	0.133
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4163
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.