5K38 | pdb_00005k38

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.4M Potassium sodium tartrate tetrahydrate

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.346	α = 90
b = 99.346	β = 90
c = 129.411	γ = 120

Symmetry
Space Group	P 61

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 315r		2014-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-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	2.05	86.04	96.98	0.077	16.31	7.3		41810

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 (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	3L0L	2.05	43.02	41810	2215	96.98	0.18581	0.18465	0.19	0.20693	0.21	RANDOM	15.928

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]
7.77			7.77		-15.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.154
r_dihedral_angle_4_deg	20.998
r_dihedral_angle_3_deg	16.12
r_dihedral_angle_1_deg	5.56
r_angle_refined_deg	1.706
r_mcangle_it	1.375
r_angle_other_deg	1.363
r_mcbond_it	0.862
r_mcbond_other	0.861
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.154
r_dihedral_angle_4_deg	20.998
r_dihedral_angle_3_deg	16.12
r_dihedral_angle_1_deg	5.56
r_angle_refined_deg	1.706
r_mcangle_it	1.375
r_angle_other_deg	1.363
r_mcbond_it	0.862
r_mcbond_other	0.861
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3707
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.