Experiment: 6T81

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.032	α = 90
b = 41.009	β = 104.13
c = 71.684	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	PIXEL	DECTRIS PILATUS 6M-F		2016-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976800	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	0.98	40.76	84.8	0.042	0.056	0.022	28.2	6.6	114851	114851

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.98	1.03	56.7		0.317	0.317	0.386	0.155	2.3	5.9

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	4HT0	0.98	39.64	103336	11479	84.62	0.1482	0.1456	0.1716	RANDOM	14.733

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]
0.72		-0.01	-0.57		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.286
r_sphericity_free	22.454
r_dihedral_angle_4_deg	21.884
r_sphericity_bonded	13.238
r_rigid_bond_restr	12.399
r_dihedral_angle_3_deg	12.279
r_dihedral_angle_1_deg	7.338
r_angle_refined_deg	2.404
r_chiral_restr	0.152
r_bond_refined_d	0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.286
r_sphericity_free	22.454
r_dihedral_angle_4_deg	21.884
r_sphericity_bonded	13.238
r_rigid_bond_restr	12.399
r_dihedral_angle_3_deg	12.279
r_dihedral_angle_1_deg	7.338
r_angle_refined_deg	2.404
r_chiral_restr	0.152
r_bond_refined_d	0.018
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2035
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
Coot	model building

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.