Experiment: 3IAL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	7.8	298	28% PEG 3350, 0.21 M MgCl2, 0.1 M Tris-HCl (pH 7.8), 10 mM ATP, 10 mM L-Proline, 1 mM TCEP; for cryoprotection, crystal-containing drop was diluted approx. four-fold with 30% glycerol, 0.175 M MgCl2, 24.5% PEG 3350, 0.105 M Tris (pH 8.2), 0.7 mM TCEP and crystal was frozen in LN2 after several minutes of equilibration., sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.338	α = 90
b = 87.624	β = 90
c = 142.41	γ = 90

Symmetry
Space Group	P 21 21 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	MarUSA MarMosaic -325 CCD		2008-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	2.2	40	98.7	0.089	8	4.5		52868		5	36.7

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	2.2	2.28	92.2		0.369	2.8	3.5	4857

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	1NJ5	2.2	30.19	52791	2726	98.72	0.174	0.172	0.1864	0.215	0.2185	RANDOM	34.624

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]
-1.53			-0.1		1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.365
r_dihedral_angle_4_deg	17.506
r_dihedral_angle_3_deg	12.427
r_dihedral_angle_1_deg	5.89
r_scangle_it	4.163
r_scbond_it	2.741
r_mcangle_it	2.23
r_mcbond_it	1.334
r_angle_refined_deg	1.07
r_angle_other_deg	0.798

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.365
r_dihedral_angle_4_deg	17.506
r_dihedral_angle_3_deg	12.427
r_dihedral_angle_1_deg	5.89
r_scangle_it	4.163
r_scbond_it	2.741
r_mcangle_it	2.23
r_mcbond_it	1.334
r_angle_refined_deg	1.07
r_angle_other_deg	0.798
r_mcbond_other	0.366
r_chiral_restr	0.062
r_bond_refined_d	0.007
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	7924
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	96

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction

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.