3L95 | pdb_00003l95

Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OO4	pdb 2OO4, fab fragment

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	292	Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.254	α = 90
b = 163.934	β = 90
c = 179.62	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	93	CCD	ADSC QUANTUM 315		2008-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.000	ALS	5.0.2

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	2.19	30	97.4	0.098	14.9	6.6	71794	69923		-3

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)
1	2.19	2.32	88.5		0.496	4.2	5.5

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 (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 2OO4, fab fragment	2.19	30	62930	6979	97.76	0.22721	0.22233	0.23	0.27076	0.27	RANDOM	27.279

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]
-1.92			0.4		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.236
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	15.618
r_dihedral_angle_1_deg	5.872
r_mcangle_it	3.579
r_scangle_it	3.199
r_mcbond_it	2.397
r_scbond_it	2.202
r_angle_refined_deg	1.139
r_angle_other_deg	0.821
r_mcbond_other	0.57
r_symmetry_vdw_other	0.197
r_symmetry_vdw_refined	0.19
r_nbd_refined	0.188
r_nbd_other	0.185
r_nbtor_refined	0.174
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.14
r_metal_ion_refined	0.119
r_nbtor_other	0.082
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9986
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	39

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling