8Y7L | pdb_00008y7l

Crystal Structure of Nur77 LBD in complex with N-(2'-(4-hydroxypiperidin-1-yl)-[4,4'-bipyridin]-2-yl)cinnamamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V3E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG4000, Sodium citrate, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.781	α = 90
b = 76.125	β = 90
c = 128.813	γ = 90

Symmetry
Space Group	P 21 21 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	DECTRIS PILATUS 6M		2023-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9792	SSRF	BL18U1

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	2.68	50	99.9	0.893	4.556	6.4		21249

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	2.68	2.73			0.898

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	2.683	33.944	21189	1069	99.802	0.206	0.2042	0.21	0.2425	0.25	39.167

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]
-0.108			0.396		-0.288

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.928
r_dihedral_angle_3_deg	19.938
r_dihedral_angle_4_deg	17.522
r_lrange_it	11.382
r_lrange_other	11.378
r_dihedral_angle_1_deg	6.256
r_scangle_it	6.089
r_scangle_other	6.088
r_mcangle_it	5.51
r_mcangle_other	5.509
r_scbond_it	3.837
r_scbond_other	3.836
r_mcbond_it	3.449
r_mcbond_other	3.442
r_angle_refined_deg	1.573
r_angle_other_deg	1.258
r_nbd_other	0.228
r_nbd_refined	0.227
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.149
r_ncsr_local_group_1	0.13
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.009
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	3621
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing