Experiment: 3LSS

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	7	298	1 ul 11 mg/ml protein in SGPP buffer mixed with 0.5 ul 2.4 M sodium malonate; crystal then soaked in 3.4 M sodium malonate (pH 7.0) supplemented with 10 mM ATP for 25 minutes before freezing., sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.652	α = 90
b = 175.652	β = 90
c = 248.518	γ = 120

Symmetry
Space Group	H 3 2

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	MARMOSAIC 325 mm CCD		2008-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979	SSRL	BL11-1

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	1.95	50	99.9	0.09	9.1	8		106754		5	37

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)
	1.95	2.02	99.6		0.808	1.5	6.4	10577

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3LSQ	1.95	34.57	106719	5392	99.91	0.169	0.168	0.179	0.195	0.202	RANDOM	50.159

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]
1.14	0.57		1.14		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.025
r_dihedral_angle_4_deg	14.559
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_1_deg	6.111
r_scangle_it	5.824
r_scbond_it	3.85
r_mcangle_it	3.252
r_mcbond_it	2.07
r_angle_refined_deg	1.331
r_angle_other_deg	0.863

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.025
r_dihedral_angle_4_deg	14.559
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_1_deg	6.111
r_scangle_it	5.824
r_scbond_it	3.85
r_mcangle_it	3.252
r_mcbond_it	2.07
r_angle_refined_deg	1.331
r_angle_other_deg	0.863
r_mcbond_other	0.659
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7265
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	77

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.