Experiment: 3F9B

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Drop: 2uL of protein solution (20mg/mL in 100mM Sodium acetate, 100mM NaCl, 1mM EDTA, 1mM DTT, pH 5.7), 0.5uL of 55mM Sodium vanadate, and 3uL of precipitant solution (12-19% PEG 3350, 0.1M Hepes pH 7.5). Well: 1000uL of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.196	α = 90
b = 58.191	β = 90
c = 90.347	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	ADSC QUANTUM 315	mirrors	2008-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	1.42	30	98.8	0.065	30.828	8.3	54027	54027			17.9

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	1.42	1.47	89.5		0.271		4.9	4789

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YPT	1.42	29.1	53940	53940	2772	99.17	0.174	0.174	0.173	0.196	RANDOM	21.046

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]
0.18			0.37		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.166
r_dihedral_angle_4_deg	16.188
r_dihedral_angle_3_deg	11.192
r_dihedral_angle_1_deg	6.113
r_scangle_it	2.996
r_scbond_it	1.978
r_angle_refined_deg	1.353
r_mcangle_it	1.348
r_mcbond_it	0.878
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.166
r_dihedral_angle_4_deg	16.188
r_dihedral_angle_3_deg	11.192
r_dihedral_angle_1_deg	6.113
r_scangle_it	2.996
r_scbond_it	1.978
r_angle_refined_deg	1.353
r_mcangle_it	1.348
r_mcbond_it	0.878
r_nbtor_refined	0.3
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.158
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.089
r_chiral_restr	0.084
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	26

Software

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