Experiment: 3KYK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B2X	PDB entry 2B2X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	2M ammonium sulfate, 0.1M sodium acetate pH 3.5 and 0.1M TCEP, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.632	α = 90
b = 90.632	β = 90
c = 215.041	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	MAR scanner 345 mm plate		2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97961	APS	31-ID

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	3.2	50	100	0.221	3.5	17.8	9320	9258	2	2

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)
	3.2	3.31	100		0.571		17.2	888

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2B2X	3.2	44.34	9331	9257	442	99.91	0.198	0.194	0.29	RANDOM	18.413

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]
-0.11	-0.05		-0.11		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.146
r_dihedral_angle_4_deg	24.045
r_dihedral_angle_3_deg	23.627
r_dihedral_angle_1_deg	8.9
r_scangle_it	3.555
r_angle_refined_deg	2.381
r_scbond_it	2.109
r_mcangle_it	1.451
r_mcbond_it	0.741
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.146
r_dihedral_angle_4_deg	24.045
r_dihedral_angle_3_deg	23.627
r_dihedral_angle_1_deg	8.9
r_scangle_it	3.555
r_angle_refined_deg	2.381
r_scbond_it	2.109
r_mcangle_it	1.451
r_mcbond_it	0.741
r_chiral_restr	0.135
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3251
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	20

Software

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