3K23 | pdb_00003k23

Glucocorticoid Receptor with Bound D-prolinamide 11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		homology model generated from PR LBD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.927	α = 90
b = 65.956	β = 103.64
c = 71.528	γ = 90

Symmetry
Space Group	C 1 2 1

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 210		2006-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-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	50	99.1	0.079	8.1	3.6	17141	16987			36.7

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	3	3.11	93.2		0.381		2.9	1565

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	homology model generated from PR LBD	3	19.82	16800	16800	1170	100	0.229	0.229	0.224	0.23	0.289	0.24	RANDOM	61.285

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]
2.12		-1.8	-3.27		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.149
r_dihedral_angle_3_deg	17.287
r_dihedral_angle_4_deg	14.544
r_dihedral_angle_1_deg	5.341
r_angle_refined_deg	1.243
r_scangle_it	0.915
r_angle_other_deg	0.85
r_mcangle_it	0.638
r_scbond_it	0.589
r_mcbond_it	0.579
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.223
r_symmetry_hbond_refined	0.194
r_nbtor_refined	0.192
r_nbd_other	0.186
r_symmetry_vdw_other	0.176
r_xyhbond_nbd_other	0.159
r_xyhbond_nbd_refined	0.156
r_nbtor_other	0.088
r_chiral_restr	0.053
r_mcbond_other	0.049
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5970
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	141

Software

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