Experiment: 3NR8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9Y	PDB ENTRY 1I9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	20% PEG 6000, 0.1M citric acid pH 5, 2mM biphenyl 2,3',4,5',6-pentakisphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.796	α = 90
b = 61.177	β = 91.9
c = 114.32	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RAYONIX MX-225	mirrors	2010-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	2.8	44.77	99.6	0.152	0.152	7.9	4.6	15400	15338			59.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	99.5		0.72	0.72	2	4.6	2227

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1I9Y	2.8	20	14621	14524	755	99.34	0.21644	0.21644	0.21358	0.22	0.27247	0.27	RANDOM	35.337

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]
-0.68		2.19	-0.38		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_4_deg	18.752
r_dihedral_angle_3_deg	16.575
r_dihedral_angle_1_deg	6.288
r_scangle_it	1.201
r_angle_refined_deg	1.146
r_angle_other_deg	0.807
r_scbond_it	0.702
r_mcangle_it	0.471
r_mcbond_it	0.245

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_4_deg	18.752
r_dihedral_angle_3_deg	16.575
r_dihedral_angle_1_deg	6.288
r_scangle_it	1.201
r_angle_refined_deg	1.146
r_angle_other_deg	0.807
r_scbond_it	0.702
r_mcangle_it	0.471
r_mcbond_it	0.245
r_chiral_restr	0.065
r_mcbond_other	0.046
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4784
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	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.