9XMJ | pdb_00009xmj

A Potent and Selective ROR gamma Inhibitor for the Treatment of Autoimmune Diseases

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8X7E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	295	80mM MES buffer (pH 6.2) in the presence of 9% PEG6,000.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.263	α = 90
b = 72.157	β = 90.025
c = 98.355	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS 2M-F		2013-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.18	50	97.1	0.133	0.995	9.81	3.8		57764

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	2.18	2.31	94.3		0.484	1.03

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.18	49.177	57764	2903	98.712	0.181	0.1795	0.1884	0.2179	0.2248	44.817

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]
-0.001		0.009	0.007		-0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.438
r_dihedral_angle_3_deg	15.103
r_lrange_it	9.614
r_lrange_other	9.61
r_scangle_it	7.851
r_scangle_other	7.85
r_dihedral_angle_2_deg	7.477
r_mcangle_it	6.977
r_mcangle_other	6.977
r_dihedral_angle_1_deg	5.572
r_scbond_it	5.516
r_scbond_other	5.515
r_mcbond_it	5.181
r_mcbond_other	5.181
r_angle_refined_deg	1.677
r_angle_other_deg	0.542
r_symmetry_nbd_refined	0.285
r_xyhbond_nbd_refined	0.244
r_nbd_refined	0.222
r_nbd_other	0.204
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.183
r_ncsr_local_group_9	0.124
r_ncsr_local_group_5	0.112
r_ncsr_local_group_10	0.112
r_ncsr_local_group_4	0.099
r_ncsr_local_group_6	0.097
r_ncsr_local_group_12	0.096
r_ncsr_local_group_1	0.081
r_ncsr_local_group_11	0.081
r_ncsr_local_group_3	0.079
r_chiral_restr	0.077
r_ncsr_local_group_7	0.077
r_symmetry_xyhbond_nbd_other	0.076
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_2	0.073
r_ncsr_local_group_8	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7824
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing