7XWR | pdb_00007xwr

Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GIU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.436	α = 90
b = 89.226	β = 90
c = 101.532	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.16	46.633	99.3	0.451	0.537	0.288	0.937	4.4	5.9		25917

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	2.16	2.23			2.186	2.664	1.499	0.623		5.7

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 (All)	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	2giu	2.164	46.633	25840	1294	98.955	0.264	0.2614	0.27	0.3178	0.33	RANDOM	26.142

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]
3.579			-9.383		5.804

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.882
r_dihedral_angle_3_deg	16.102
r_dihedral_angle_4_deg	15.571
r_dihedral_angle_1_deg	6.291
r_lrange_it	5.798
r_lrange_other	5.798
r_scangle_it	3.937
r_scangle_other	3.936
r_mcangle_it	3.581
r_mcangle_other	3.581
r_scbond_it	2.432
r_scbond_other	2.432
r_mcbond_it	2.245
r_mcbond_other	2.244
r_angle_refined_deg	1.555
r_angle_other_deg	1.289
r_symmetry_xyhbond_nbd_refined	0.501
r_symmetry_nbd_refined	0.293
r_nbd_other	0.263
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.183
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.16
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3530
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing