Experiment: 5NB0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T60

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	6% PEG3350, BisTrisPropane pH 7.5 and MgCl2 0.2 M

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.518	α = 90
b = 131.518	β = 90
c = 248.855	γ = 120

Symmetry
Space Group	H 3

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	RAYONIX MX-225		2010-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	51.783	98.4	0.084	0.11	0.069	11.2	2.2	43361	43361

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	95		0.264	0.264	0.347	0.223	2.1	2.1

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	1T60	2.7	51.78	41166	2182	98.27	0.1639	0.1633	0.16	0.1758	0.16	RANDOM	26.648

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]
-5.37			-5.37		10.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.302
r_dihedral_angle_3_deg	16.912
r_dihedral_angle_4_deg	16.08
r_dihedral_angle_1_deg	5.563
r_angle_refined_deg	1.146
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13886
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.