5CZV

Crystal structure of Notch3 NRR in complex with 20350 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ETOPDB entry 3ETO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.1M NaAc, pH 5.6, 17.5% (v/v) PEG3000
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.917α = 90
b = 104.349β = 113.17
c = 92.849γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.193086.40.1264.82.61161457.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.193.2679.10.2722.4539

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3ETO3.1929.621161256785.940.20620.20360.2565RANDOM68.65
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]
8.2877-2.41354.8788-13.1665
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.34
t_omega_torsion3.19
t_angle_deg1.23
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.34
t_omega_torsion3.19
t_angle_deg1.23
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4915
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms17

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement