9W12 | pdb_00009w12

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with ZOL-P

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Y8G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	18% (w/v) PEG 3350, 0.25 M Ammonium sulfate, and 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.753	α = 90
b = 102.43	β = 90
c = 195.933	γ = 90

Symmetry
Space Group	C 2 2 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	Bruker PHOTON III		2025-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	1.75	25	98.9	0.996	23.098	5		53081

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	1.75	1.81			0.873

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	1.75	24.79	50392	2648	98.43	0.16815	0.16669	0.1787	0.19661	0.2029	RANDOM	35.013

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]
0.04			1.56		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.264
r_dihedral_angle_4_deg	24.565
r_dihedral_angle_3_deg	13.948
r_long_range_B_other	8.391
r_long_range_B_refined	8.387
r_scangle_other	7.026
r_dihedral_angle_1_deg	5.744
r_scbond_it	4.737
r_scbond_other	4.735
r_mcangle_it	4.198
r_mcangle_other	4.198
r_mcbond_it	3.128
r_mcbond_other	3.125
r_angle_refined_deg	1.708
r_angle_other_deg	1.525
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3940
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SAINT	data scaling
PHASER	phasing