7ABV | pdb_00007abv

Structure of the S1-cleaved mouse Notch1 Negative Regulatory Region (NRR)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	2.0 M sodium chloride, 0.1 M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.724	α = 90
b = 65.724	β = 90
c = 161.683	γ = 90

Symmetry
Space Group	P 42 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.06998	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.065	60.886	91.5	0.105	0.109	0.03	0.999	14.6	12.9		15144

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.065	2.296	64.6		1.431	1.496	0.43	0.77		11.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	3ETO	2.065	60.885	15143	795	66.922	0.198	0.196	0.2	0.2375	0.24	57.792

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]
-0.597			-0.597		1.194

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.74
r_dihedral_angle_4_deg	28.636
r_dihedral_angle_3_deg	15.268
r_dihedral_angle_1_deg	7.389
r_lrange_it	6.218
r_scangle_it	3.461
r_mcangle_it	2.72
r_scbond_it	2.196
r_mcbond_it	1.623
r_angle_refined_deg	1.501
r_nbtor_refined	0.317
r_nbd_refined	0.235
r_symmetry_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.129
r_chiral_restr	0.104
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1796
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
STARANISO	data scaling
Aimless	data scaling
XDS	data reduction
autoPROC	data processing