Experiment: 3BE4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AK2	PDB entry 1AK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	2.5 M Ammonium sulfate, 0.1 M BTP pH 7.0, 10 mM Adenosine-5-pentaphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.175	α = 90
b = 101.175	β = 90
c = 72.433	γ = 120

Symmetry
Space Group	H 3

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 315		2007-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

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	1.6	20	99	0.067	0.057	11	3.6	36167	36167			19.543

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	1.6	1.66	100		0.466	0.438	3.35	3.7	3686

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 1AK2	1.6	19.37	36130	36130	1814	98.98	0.164	0.162	0.16	0.202	0.2	RANDOM	25.453

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]
0.02	0.01		0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.836
r_dihedral_angle_4_deg	18.141
r_dihedral_angle_3_deg	15.529
r_dihedral_angle_1_deg	6.95
r_scangle_it	5.429
r_scbond_it	3.965
r_angle_refined_deg	2.939
r_mcangle_it	2.748
r_mcbond_it	1.98
r_symmetry_hbond_refined	0.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.836
r_dihedral_angle_4_deg	18.141
r_dihedral_angle_3_deg	15.529
r_dihedral_angle_1_deg	6.95
r_scangle_it	5.429
r_scbond_it	3.965
r_angle_refined_deg	2.939
r_mcangle_it	2.748
r_mcbond_it	1.98
r_symmetry_hbond_refined	0.412
r_chiral_restr	0.37
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.268
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.213
r_bond_refined_d	0.035
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1655
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	70

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.