3KZZ

Crystal structure of SNAP-tag bound to its substrate benzylguanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KZYPDB ENTRY 3KZY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529132% PEG3350, 100 mM BisTris pH 6.5, 400 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4950.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.16α = 90
b = 77.16β = 90
c = 64.81γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979653ESRFBM30A

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
11.895099.70.06132.179.2161551610029.64
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)
1.892.0198.70.2786.119.22505

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3KZY1.8938.5816098152938051000.188840.18710.22215RANDOM25.838
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.978
r_dihedral_angle_4_deg23.877
r_dihedral_angle_3_deg13.18
r_dihedral_angle_1_deg5.969
r_scangle_it3.689
r_scbond_it2.295
r_mcangle_it1.576
r_angle_refined_deg1.483
r_mcbond_it0.902
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.978
r_dihedral_angle_4_deg23.877
r_dihedral_angle_3_deg13.18
r_dihedral_angle_1_deg5.969
r_scangle_it3.689
r_scbond_it2.295
r_mcangle_it1.576
r_angle_refined_deg1.483
r_mcbond_it0.902
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1215
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms19

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing