Experiment: 4XKV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1 M Tris-HCl, 3.5 M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.917	α = 90
b = 73.917	β = 90
c = 174.502	γ = 120

Symmetry
Space Group	P 3 2 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	PIXEL	DECTRIS PILATUS 6M	mirrors	2014-01-28	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)	Rpim I (All)	CC (Half)	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	2.1	43.05	80.1	0.08	0.043	0.995	10.1	3.5		26540

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	75.7		0.202	0.116	0.936	4.2	2.9	1994

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	4xm3	2.1	43.05	26530	1354	80.09	0.2296	0.2267	0.2819	RANDOM	22.591

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]
0.63	0.32		0.63		-2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_4_deg	16.798
r_dihedral_angle_3_deg	12.439
r_dihedral_angle_1_deg	6.267
r_angle_refined_deg	0.998
r_angle_other_deg	0.699
r_mcangle_it	0.374
r_mcbond_it	0.214
r_mcbond_other	0.214
r_chiral_restr	0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_4_deg	16.798
r_dihedral_angle_3_deg	12.439
r_dihedral_angle_1_deg	6.267
r_angle_refined_deg	0.998
r_angle_other_deg	0.699
r_mcangle_it	0.374
r_mcbond_it	0.214
r_mcbond_other	0.214
r_chiral_restr	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4523
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	18

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	phasing
ARP	model building
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	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 R01GM133198.