9VVN | pdb_00009vvn

Crystal structure of computationally designed protein VTP-4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.01M NiCl2, 0.1M Tris-HCl pH8.5, 20% w/v Polyethylene glycol Monomethyl ether 2,000
Crystal Properties
Matthews coefficientSolvent content
2.1442.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.606α = 90
b = 58.488β = 90
c = 83.828γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2024-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU0.999990SPring-8BL45XU

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
11.647.9799.90.08514.91123836
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)
11.61.630.996

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.647.96723781116999.8280.210.20730.21880.25460.264524.626
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]
0.008-0.2180.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.136
r_dihedral_angle_3_deg12.28
r_lrange_it7.495
r_lrange_other7.438
r_dihedral_angle_1_deg6.13
r_scangle_it5.814
r_scangle_other5.811
r_dihedral_angle_2_deg5.773
r_scbond_it3.795
r_scbond_other3.792
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.136
r_dihedral_angle_3_deg12.28
r_lrange_it7.495
r_lrange_other7.438
r_dihedral_angle_1_deg6.13
r_scangle_it5.814
r_scangle_other5.811
r_dihedral_angle_2_deg5.773
r_scbond_it3.795
r_scbond_other3.792
r_mcangle_other3.49
r_mcangle_it3.486
r_mcbond_it2.527
r_mcbond_other2.527
r_angle_refined_deg2.003
r_angle_other_deg0.625
r_symmetry_xyhbond_nbd_refined0.265
r_symmetry_nbd_refined0.218
r_nbd_refined0.213
r_symmetry_nbd_other0.201
r_xyhbond_nbd_refined0.2
r_nbtor_refined0.191
r_nbd_other0.19
r_symmetry_nbtor_other0.089
r_chiral_restr0.085
r_symmetry_xyhbond_nbd_other0.084
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1308
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing