8Z5A | pdb_00008z5a

Crystal Structure of Nur77 LBD in complex with NLM1

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
3.58	65.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.463	α = 90
b = 76.435	β = 90
c = 127.866	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		2022-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

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	2.179	50	100	0.154	24.182	11.4		38870

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	2.179	2.22			0.822

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	2.179	37.259	38784	1906	99.81	0.241	0.239	0.2403	0.2738	0.2724	48.876

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]
0.408			1.705		-2.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.262
r_dihedral_angle_3_deg	19.293
r_dihedral_angle_4_deg	16.823
r_lrange_it	10.217
r_lrange_other	10.216
r_scangle_it	7.218
r_scangle_other	7.217
r_dihedral_angle_1_deg	6.009
r_mcangle_it	5.877
r_mcangle_other	5.875
r_scbond_it	4.949
r_scbond_other	4.948
r_mcbond_it	4.302
r_mcbond_other	4.301
r_angle_refined_deg	1.612
r_angle_other_deg	1.284
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.206
r_nbd_other	0.199
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.167
r_ncsr_local_group_1	0.152
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_xyhbond_nbd_other	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	3584
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	42

Software

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