Experiment: 2PNO

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M Hepes/NaOH, 30%(v/v) PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.5	α = 90
b = 293.9	β = 90
c = 206.5	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 210		2006-10-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-11-13	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0	SPring-8	BL44B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.97904, 0.97949, 0.96423, 0.99519	SPring-8	BL44B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.3	50	99.9	0.08	20.3	7.5		54085			97.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	3.3	3.48	100		0.443	4.3	7.6	7797

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	3.3	15	50769	2675	99.99	0.22281	0.22109	0.25462	RANDOM	65.104

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]
-0.1			1.55		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.226
r_dihedral_angle_3_deg	18.876
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_1_deg	3.696
r_scangle_it	2.907
r_scbond_it	1.674
r_mcangle_it	1.196
r_angle_refined_deg	0.975
r_mcbond_it	0.659
r_nbtor_refined	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.226
r_dihedral_angle_3_deg	18.876
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_1_deg	3.696
r_scangle_it	2.907
r_scbond_it	1.674
r_mcangle_it	1.196
r_angle_refined_deg	0.975
r_mcbond_it	0.659
r_nbtor_refined	0.329
r_symmetry_hbond_refined	0.318
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13353
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1170

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.