Experiment: 6XK0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	Prior to crystallization, 15 mg/ml protein was incubated with dexamethasone powder (10-fold molar excess) for 60 min at room temperature, and the mixture with the powder in suspension was used for crystallization. 1 ul of this mixture was mixed with 1 ul of the well condition (1.8 M ammonium dihydrogen citrate, pH 7.0) and equilibrated against the well solution in 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 1:1 mixture of Paratone N and mineral oil was used as a cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.983	α = 90
b = 94.983	β = 90
c = 143.591	γ = 120

Symmetry
Space Group	P 61

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		2011-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.979	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	50	99.8	0.11	0.123	0.055	8.8	4.9		28870		-3	40

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	98.3		1.053	1.221	0.605	0.619		3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3V08	2.4	47.54	22871	1132	83.67	0.2054	0.2033	0.2492	RANDOM	56.799

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]
-0.05	-0.02		-0.05		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.544
r_dihedral_angle_4_deg	17.818
r_dihedral_angle_3_deg	13.695
r_dihedral_angle_1_deg	4.967
r_angle_other_deg	1.148
r_angle_refined_deg	1.127
r_chiral_restr	0.041
r_bond_other_d	0.003
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.544
r_dihedral_angle_4_deg	17.818
r_dihedral_angle_3_deg	13.695
r_dihedral_angle_1_deg	4.967
r_angle_other_deg	1.148
r_angle_refined_deg	1.127
r_chiral_restr	0.041
r_bond_other_d	0.003
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4589
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	61

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
SCALEPACK	data scaling
Coot	model building

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.