Experiment: 5NBP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM MES pH 6 200 mM LiCl2 15-25 % w/v PEG-6000

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.342	α = 90
b = 60.149	β = 93.75
c = 49.673	γ = 90

Symmetry
Space Group	C 1 2 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		2016-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	49.57	99	0.066	0.994	10.8	3.9		45347	0.094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	99		0.735	0.499	0.516	1.7	3.9

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	FOURIER SYNTHESIS	THROUGHOUT	5NBO	1.8	49.57	45346	2384	98.93	0.1769	0.175	0.2129	RANDOM	22.191

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]
1.01		0.78	-0.78		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.842
r_dihedral_angle_3_deg	13.455
r_dihedral_angle_4_deg	11.071
r_dihedral_angle_1_deg	7.207
r_angle_other_deg	3.813
r_mcangle_it	2.046
r_angle_refined_deg	1.636
r_mcbond_it	1.384
r_mcbond_other	1.379
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.842
r_dihedral_angle_3_deg	13.455
r_dihedral_angle_4_deg	11.071
r_dihedral_angle_1_deg	7.207
r_angle_other_deg	3.813
r_mcangle_it	2.046
r_angle_refined_deg	1.636
r_mcbond_it	1.384
r_mcbond_other	1.379
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_other	0.011
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3749
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	93

Software

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

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.