Experiment: 3KGR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GI7	Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5
experimental model	PDB	2D3V	Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5
experimental model	PDB	1UGN	Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5
experimental model	PDB	2GW5	Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.3	291	25-30% PEG-1500, 100mM succinic acid, 100mM sodium dihydrogen phosphate, 100mM glycine, 10mM CoCl2, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.395	α = 90
b = 69.395	β = 90
c = 54.258	γ = 120

Symmetry
Space Group	P 32

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 315r		2007-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0396	ESRF	ID23-1

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	1.8	60.098	96.3	0.067	0.067	20.2	5.5		26097		-3.7	17.458

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	1.8	1.9	78.4		0.208	0.208	3.5	3.9	3098

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5	1.8	34.698	2.05	26079	1319	96.28	0.1242	0.124	0.123	0.157	random	23.233

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]
0.565			0.565		-1.752

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.379
f_angle_d	1.279
f_chiral_restr	0.079
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2320
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	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.