Experiment: 7Q9E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	PEG 3350, lithium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.69	α = 95.36
b = 82.87	β = 90
c = 84.86	γ = 90

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	PIXEL	DECTRIS PILATUS 6M		2014-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.97916	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.7	25.92	88.9	0.066	0.079	0.043	0.996	7.05	3.3		168988			18.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79			0.307	0.367	0.199	0.92	2.11

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4YT3	1.7	25.82	160539	8441	88.88	0.1707	0.1689	0.18	0.2059	0.22	RANDOM	22.634

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]
1.68	0.04	0.23	-0.83	-1.32	-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.879
r_dihedral_angle_4_deg	16.391
r_dihedral_angle_3_deg	13.781
r_dihedral_angle_1_deg	6.695
r_angle_refined_deg	1.662
r_angle_other_deg	1.483
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.879
r_dihedral_angle_4_deg	16.391
r_dihedral_angle_3_deg	13.781
r_dihedral_angle_1_deg	6.695
r_angle_refined_deg	1.662
r_angle_other_deg	1.483
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12597
Nucleic Acid Atoms
Solvent Atoms	1022
Heterogen Atoms	285

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
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.