6Q2W | pdb_00006q2w

Crystal structure of human ROR gamma LBD in complex with a quinoline sulfonamide inverse agonist

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.1M MgCl2, 0.1M Mes pH 6, 8% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.12	α = 90
b = 56.2	β = 125.06
c = 81.4	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS PILATUS 6M		2012-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.981	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.99	46.2	99.1	0.077	0.09	0.996	10.1	3.678		32496			36.172

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.11	97.4		0.326	0.383	0.961	2.63	3.452

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	3B0W	1.99	46.2	30868	1625	99.5	0.1896	0.1873	0.19	0.2324	0.24	RANDOM	39.927

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]
-3.94		0.1	-1.81		2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.184
r_dihedral_angle_4_deg	22.533
r_dihedral_angle_3_deg	16.359
r_dihedral_angle_1_deg	5.682
r_angle_refined_deg	1.64
r_angle_other_deg	1.38
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.184
r_dihedral_angle_4_deg	22.533
r_dihedral_angle_3_deg	16.359
r_dihedral_angle_1_deg	5.682
r_angle_refined_deg	1.64
r_angle_other_deg	1.38
r_chiral_restr	0.084
r_bond_refined_d	0.008
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	3569
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	82

Software

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

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.