9KUE | pdb_00009kue

Crystal structure of the soluble green pigment protein from Tettigonia cantans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2880.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 30% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.57α = 90
b = 87.256β = 90
c = 167.609γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 12M2024-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17UM0.9792SSRFBL17UM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9947.5799.90.3070.3130.0620.9968.624.948786
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0499.21.7961.8630.4890.41214.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9931.646216245699.850.225360.223180.22820.266790.2637RANDOM38.229
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]
2.13-1.28-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.692
r_dihedral_angle_2_deg12.732
r_dihedral_angle_1_deg8.966
r_long_range_B_refined4.848
r_long_range_B_other4.826
r_scangle_other2.782
r_mcangle_it2.238
r_mcangle_other2.238
r_angle_refined_deg2.107
r_scbond_it1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.692
r_dihedral_angle_2_deg12.732
r_dihedral_angle_1_deg8.966
r_long_range_B_refined4.848
r_long_range_B_other4.826
r_scangle_other2.782
r_mcangle_it2.238
r_mcangle_other2.238
r_angle_refined_deg2.107
r_scbond_it1.85
r_scbond_other1.716
r_mcbond_it1.386
r_mcbond_other1.385
r_angle_other_deg1.016
r_chiral_restr0.106
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.004
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5259
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms390

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing