1YJE | pdb_00001yje

Crystal structure of the rNGFI-B ligand-binding domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PDU	PDB ebtry 1PDU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	NaCl, BisTris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.86	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.422	α = 90
b = 90.422	β = 90
c = 140.637	γ = 90

Symmetry
Space Group	I 41 2 2

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	MARRESEARCH	sagittal bender (mirror)	2003-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00003	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	40	98.3	0.058	20.8	8.5	11697	11676	1	1	66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.54	97.1		0.441	5.1		11676

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ebtry 1PDU	2.4	20	1	11676	11092	584	100	0.246	0.246	0.243	0.24	0.278	0.27	RANDOM	67.445

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]
0.14			0.14		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.141
r_dihedral_angle_4_deg	25.118
r_dihedral_angle_3_deg	20.088
r_dihedral_angle_1_deg	6.542
r_scangle_it	3.323
r_scbond_it	2.148
r_mcangle_it	1.779
r_angle_refined_deg	1.521
r_mcbond_it	0.985
r_symmetry_hbond_refined	0.582
r_nbtor_refined	0.312
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1726
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
AMoRE	phasing