Experiment: 3GKT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q1F	PDB ENTRY 1Q1F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.6M ammonium sulphate, 0.1M MES, pH6.5, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.8	α = 90
b = 88.8	β = 90
c = 113.5	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 225 mm CCD		2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.86437	BESSY	14.1

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	1.86	30	99.7	0.05		6.17		14316	3	3	35.127

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	1.86	2.1	100		0.35	5.03

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1Q1F	1.86	19.55	14315	13599	716	100	0.256	0.17451	0.17275	0.20839	RANDOM	28.535

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]
-0.25	-0.13		-0.25		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.319
r_dihedral_angle_4_deg	14.071
r_dihedral_angle_3_deg	13.731
r_dihedral_angle_1_deg	4.539
r_scangle_it	2.807
r_scbond_it	2.033
r_angle_refined_deg	1.452
r_mcangle_it	1.283
r_mcbond_it	0.761
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.319
r_dihedral_angle_4_deg	14.071
r_dihedral_angle_3_deg	13.731
r_dihedral_angle_1_deg	4.539
r_scangle_it	2.807
r_scbond_it	2.033
r_angle_refined_deg	1.452
r_mcangle_it	1.283
r_mcbond_it	0.761
r_nbtor_refined	0.298
r_xyhbond_nbd_refined	0.269
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.184
r_symmetry_vdw_refined	0.166
r_metal_ion_refined	0.113
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1149
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	50

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	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.