2GPP | pdb_00002gpp

Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GP7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.81	α = 90
b = 203.81	β = 90
c = 53.46	γ = 120

Symmetry
Space Group	H 3

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	MAR CCD 165 mm			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	2.6	50	98.8	0.064		9.5	25371	25066	-3	-3

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)
	2.6	2.64		84.9	0.403		3.2

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	2GP7	2.6	45.74	25372	25065	764	98.79	0.233	0.233	0.232	0.24	0.257	0.26	RANDOM	44.602

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]
-0.86	-0.43		-0.86		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.503
r_dihedral_angle_3_deg	15.579
r_dihedral_angle_4_deg	14.94
r_dihedral_angle_1_deg	5.576
r_scangle_it	1.911
r_scbond_it	1.222
r_angle_refined_deg	1.215
r_mcangle_it	0.939
r_angle_other_deg	0.733
r_mcbond_it	0.609
r_nbd_refined	0.23
r_symmetry_vdw_other	0.198
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.178
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.149
r_mcbond_other	0.146
r_nbtor_other	0.088
r_chiral_restr	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.003
r_symmetry_hbond_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	3760
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	21

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection