Experiment: 3NMJ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	30% PEG 400, 0.1 M Tris, 0.2 ammonium sulfate, 6.2 mM nickel sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.291	α = 90
b = 99.291	β = 90
c = 109.317	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	ADSC QUANTUM 315r		2009-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	85.99	100	0.178	8	9.9	11200	11200	1.4	1.4

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)
	3.1	3.27	100		0.433	0.433	1.4	9.8	1610

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.1	85.99	11170	11169	776	99.99	0.1963	0.1963	0.1932	0.2382	RANDOM	53.6081

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.959
r_dihedral_angle_4_deg	28.389
r_dihedral_angle_3_deg	24.77
r_dihedral_angle_1_deg	7.569
r_scangle_it	5.801
r_scbond_it	3.517
r_mcangle_it	2.034
r_mcbond_it	0.98
r_angle_refined_deg	0.742
r_chiral_restr	0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.959
r_dihedral_angle_4_deg	28.389
r_dihedral_angle_3_deg	24.77
r_dihedral_angle_1_deg	7.569
r_scangle_it	5.801
r_scbond_it	3.517
r_mcangle_it	2.034
r_mcbond_it	0.98
r_angle_refined_deg	0.742
r_chiral_restr	0.055
r_gen_planes_refined	0.013
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3187
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	246

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

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.