Experiment: 3NIE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N9X	pdb entry 3N9X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	22% PEG 3350, 0.175 M disodium tartrate, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.388	α = 90
b = 107.355	β = 109.65
c = 70.787	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	RIGAKU SATURN A200		2010-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	50	95.4	0.05	7.2	3.7	39641	37818	1	1	53.2

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	2.34	85.7		0.338		3	1719

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 (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 3N9X	2.3	50	39772	37792	1906	95.02	0.2254	0.2231	0.22	0.2681	0.26	RANDOM	48.6944

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]
-5.06		-0.53	3.96		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.76
r_dihedral_angle_4_deg	17.323
r_dihedral_angle_3_deg	16.197
r_dihedral_angle_1_deg	5.863
r_scangle_it	2.213
r_scbond_it	1.361
r_angle_refined_deg	1.28
r_mcangle_it	1.112
r_angle_other_deg	0.863
r_mcbond_it	0.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.76
r_dihedral_angle_4_deg	17.323
r_dihedral_angle_3_deg	16.197
r_dihedral_angle_1_deg	5.863
r_scangle_it	2.213
r_scbond_it	1.361
r_angle_refined_deg	1.28
r_mcangle_it	1.112
r_angle_other_deg	0.863
r_mcbond_it	0.601
r_mcbond_other	0.089
r_chiral_restr	0.07
r_bond_refined_d	0.011
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	5808
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.