Experiment: 6NCI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q1P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1 M Tris-HCl pH 8.5, 0.2 to 0.3 M Lithium sulfate, 26 to 29% PEG-4000

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.771	α = 90
b = 67.008	β = 90
c = 111.426	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 EIGER X 16M		2018-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-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	2.08	29.47	98.8	0.136	0.142	0.039	0.998	14.4	13		28297

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	2.08	2.13	84.5		0.942	0.985	0.28	0.818		11.2

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	3Q1P	2.08	29.47	26741	1502	98.8	0.1741	0.1712	0.18	0.2226	0.23	RANDOM	33.807

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]
1.29			0.55		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.488
r_dihedral_angle_3_deg	15.881
r_dihedral_angle_4_deg	8.055
r_dihedral_angle_1_deg	6.85
r_angle_refined_deg	1.507
r_angle_other_deg	1.436
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.488
r_dihedral_angle_3_deg	15.881
r_dihedral_angle_4_deg	8.055
r_dihedral_angle_1_deg	6.85
r_angle_refined_deg	1.507
r_angle_other_deg	1.436
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3274
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	52

Software

Software
Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.