3KBA | pdb_00003kba

Progesterone receptor bound to sulfonamide pyrrolidine partial agonist

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	20% PEG 3350, 2mM Li2SO4, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.394	α = 90
b = 64.349	β = 96.53
c = 70.42	γ = 90

Symmetry
Space Group	P 1 21 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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0000	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	1.9	50	97.2	0.064	8.6	3.5		39206

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	1.9	1.97	84.9		0.387		2.8	3394

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2	50	34246	1752	98.93	0.197	0.194	0.22	0.25	0.27	RANDOM	34.966

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]
3.94		2.26	-1.72		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.238
r_dihedral_angle_3_deg	12.559
r_dihedral_angle_4_deg	11.525
r_dihedral_angle_1_deg	4.599
r_scangle_it	1.022
r_angle_refined_deg	0.875
r_angle_other_deg	0.795
r_scbond_it	0.648
r_mcangle_it	0.446
r_mcbond_it	0.274
r_symmetry_vdw_other	0.242
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.181
r_nbtor_refined	0.171
r_nbd_other	0.16
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.104
r_nbtor_other	0.084
r_chiral_restr	0.046
r_mcbond_other	0.04
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3942
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	59

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection