7QVK

NM-02 in complex with HER2-ECD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MY6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529113% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
3.57876865.65199

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.767α = 90
b = 105.767β = 90
c = 185.882γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96872DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.165.3241000.995.119.222490101.26
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.311000.340.719.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5MY63.165.32422447118699.8580.2780.27470.27510.3299Random selection105.683
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]
-3.441-1.721-3.44111.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_3_deg17.891
r_dihedral_angle_4_deg12.787
r_lrange_it11.966
r_lrange_other11.966
r_mcangle_it8.358
r_mcangle_other8.357
r_scangle_it7.346
r_scangle_other7.345
r_dihedral_angle_1_deg6.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_3_deg17.891
r_dihedral_angle_4_deg12.787
r_lrange_it11.966
r_lrange_other11.966
r_mcangle_it8.358
r_mcangle_other8.357
r_scangle_it7.346
r_scangle_other7.345
r_dihedral_angle_1_deg6.404
r_mcbond_other5.053
r_mcbond_it5.052
r_scbond_it4.345
r_scbond_other4.345
r_angle_other_deg2.586
r_angle_refined_deg1.406
r_symmetry_xyhbond_nbd_refined0.586
r_symmetry_nbd_other0.251
r_nbd_refined0.223
r_xyhbond_nbd_refined0.193
r_nbd_other0.192
r_nbtor_refined0.161
r_xyhbond_nbd_other0.142
r_symmetry_nbd_refined0.107
r_symmetry_xyhbond_nbd_other0.082
r_symmetry_nbtor_other0.074
r_chiral_restr0.05
r_bond_other_d0.036
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4783
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing