4CUD | pdb_00004cud

Human Notch1 EGF domains 11-13 mutant fucosylated at T466


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VJ3PDB ENTRY 2VJ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.2144.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.29α = 90
b = 28.29β = 90
c = 282.732γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.8524.1493.50.073.310837
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)
11.851.995.30.4235.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VJ31.8524.141083754091.940.225720.224060.220.259920.26RANDOM23.172
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.396
r_dihedral_angle_4_deg24.57
r_dihedral_angle_3_deg11.661
r_dihedral_angle_1_deg5.623
r_angle_refined_deg1.112
r_symmetry_vdw_refined0.22
r_nbd_refined0.215
r_symmetry_hbond_refined0.107
r_metal_ion_refined0.096
r_xyhbond_nbd_refined0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.396
r_dihedral_angle_4_deg24.57
r_dihedral_angle_3_deg11.661
r_dihedral_angle_1_deg5.623
r_angle_refined_deg1.112
r_symmetry_vdw_refined0.22
r_nbd_refined0.215
r_symmetry_hbond_refined0.107
r_metal_ion_refined0.096
r_xyhbond_nbd_refined0.082
r_chiral_restr0.072
r_symmetry_metal_ion_refined0.064
r_nbtor_refined0.032
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms914
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing