7XVY | pdb_00007xvy

Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN

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
2.02	39.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.194	α = 90
b = 89.014	β = 90
c = 101.328	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		2019-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.54	46.443	99.6	0.998	18.7	11.6		69739

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57			0.577

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	1.544	46.443	69667	3392	99.514	0.208	0.2063	0.22	0.2375	0.25	RANDOM	19.881

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]
-0.187			0.17		0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.464
r_dihedral_angle_3_deg	16.108
r_dihedral_angle_2_deg	12.634
r_lrange_it	6.161
r_lrange_other	6.16
r_dihedral_angle_1_deg	5.546
r_scangle_it	4.996
r_scangle_other	4.995
r_scbond_it	3.351
r_scbond_other	3.35
r_mcangle_it	3.099
r_mcangle_other	3.099
r_mcbond_it	2.225
r_mcbond_other	2.225
r_angle_refined_deg	1.738
r_angle_other_deg	0.583
r_symmetry_nbd_refined	0.28
r_nbd_refined	0.246
r_nbd_other	0.238
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.175
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3543
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
MOLREP	phasing