2OO4 | pdb_00002oo4

Structure of LNR-HD (Negative Regulatory Region) from human Notch 2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	298	100 mM BisTris, 200mM MgCl2, 18% PEG3350, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2			298	100mM Tris, 200mM MgCl2, 24% PEG3350, 10% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.372	α = 90
b = 74.706	β = 90
c = 139.412	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	77.2	CCD	ADSC QUANTUM 315	BEAMLINE X29 FEATURES HIGH- FLUX RADIATION DERIVED FROM A 54-POLE HARMONIC EMISSION UNDULATOR, A VERTICALLY FOCUSING MIRROR AND A HORIZONTALLY FOCUSING MONOCHROMATOR	2006-02-25	M	SINGLE WAVELENGTH
2	1	x-ray	77.2	M	SINGLE WAVELENGTH
3	1	x-ray	77.2	M	SINGLE WAVELENGTH
4	1	x-ray	77.2	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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
1,2,3,4	2.003	30	97.2	0.075	15.5	4.9		31791			33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4	2.003	2.07	98.1		0.405		4.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2.003	30	31732	1603	97.1	0.229	0.226	0.23	0.268	0.26	RANDOM	49.12

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]
0.22			-0.88		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.916
r_dihedral_angle_4_deg	14.322
r_dihedral_angle_3_deg	13.579
r_dihedral_angle_1_deg	5.348
r_scangle_it	1.645
r_angle_refined_deg	1.174
r_scbond_it	1.088
r_mcangle_it	0.677
r_mcbond_it	0.403
r_nbtor_refined	0.298
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.133
r_metal_ion_refined	0.131
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.088
r_symmetry_hbond_refined	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3411
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	67

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction