Experiment: 3NBX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES pH 6.5, 2 mM ATP, 10 mM MgCl2, 0.1-0.6 M ammonium sulfate, 10-20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.232	α = 90
b = 162.232	β = 90
c = 55.316	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	1 collimating mirror, 1 focusing toroidal mirror Si(111) double crystal monochromator	2007-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.004	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.91	29.7	99.19	0.065	0.065	25	5.7	18552	18402			88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.91	3.04	95.6		2.9	3.4	2268

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SIRAS	THROUGHOUT	2.91	29.7	18552	17463	939	99.31	0.22574	0.22345	0.26923	RANDOM	74.216

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]
-2.31	-1.16		-2.31		3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.433
r_dihedral_angle_4_deg	17.991
r_dihedral_angle_3_deg	17.851
r_dihedral_angle_1_deg	4.579
r_angle_refined_deg	0.97
r_nbtor_refined	0.295
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.113
r_xyhbond_nbd_refined	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.433
r_dihedral_angle_4_deg	17.991
r_dihedral_angle_3_deg	17.851
r_dihedral_angle_1_deg	4.579
r_angle_refined_deg	0.97
r_nbtor_refined	0.295
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.113
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3847
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DNA	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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 R01GM157729.