Experiment: 6NPZ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.321	α = 90
b = 56.088	β = 104.56
c = 92.019	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 EIGER X 9M		2017-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.99958	NSLS-II	17-ID-1

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	2.12	29.82	98.5	0.11	0.119	0.046	0.996	10.2	6.8		48316

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	2.12	2.18	83.5		0.721	0.782	0.297	0.838		6.6

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 6BUU	2.12	29.82	45932	2364	99.03	0.1881	0.1853	0.2	0.241	0.24	RANDOM	39.787

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]
-0.15		1.28	-0.72		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.454
r_dihedral_angle_4_deg	19.924
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_1_deg	7.045
r_angle_refined_deg	2.06
r_angle_other_deg	1.517
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.454
r_dihedral_angle_4_deg	19.924
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_1_deg	7.045
r_angle_refined_deg	2.06
r_angle_other_deg	1.517
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.009
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5514
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	35

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.