4DOR | pdb_00004dor

Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	298	9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.522	α = 90
b = 59.439	β = 100.13
c = 74.201	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	CCD	MARMOSAIC 300 mm CCD		2010-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	45	99.9	13	3.9	42849	42806

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.9	27.67	42849	42702	2149	99.35	0.1755	0.1755	0.1732	0.19	0.2196	0.23	RANDOM	24.3912

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]
-0.49		0.36	-0.16		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.363
r_dihedral_angle_4_deg	23.734
r_dihedral_angle_3_deg	13.515
r_sphericity_free	8.293
r_sphericity_bonded	6.071
r_dihedral_angle_1_deg	4.621
r_rigid_bond_restr	4.293
r_angle_refined_deg	1.255
r_chiral_restr	0.089
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.363
r_dihedral_angle_4_deg	23.734
r_dihedral_angle_3_deg	13.515
r_sphericity_free	8.293
r_sphericity_bonded	6.071
r_dihedral_angle_1_deg	4.621
r_rigid_bond_restr	4.293
r_angle_refined_deg	1.255
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3882
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	47

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
DENZO	data reduction
HKL-2000	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.