Experiment: 6PT6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PT4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	PEG 4000, Hepes, sodium acetate trihydrate, arginine, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.728	α = 90
b = 102.211	β = 90
c = 170.745	γ = 90

Symmetry
Space Group	P 21 21 21

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 200K		2016-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.25	50	95.3	0.096	0.994	14.6	4		46858

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	2.25	2.29			0.292

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	6PT4	2.25	31.78	45724	2387	98.61	0.2027	0.2002	0.2516	RANDOM	30.727

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]
-0.33			0.17		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.081
r_dihedral_angle_4_deg	17.591
r_dihedral_angle_3_deg	14.051
r_dihedral_angle_1_deg	7.428
r_angle_refined_deg	1.698
r_angle_other_deg	1.35
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.081
r_dihedral_angle_4_deg	17.591
r_dihedral_angle_3_deg	14.051
r_dihedral_angle_1_deg	7.428
r_angle_refined_deg	1.698
r_angle_other_deg	1.35
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7513
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.