2VBN

Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G9ZPDB ENTRY 1G9Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.54 MG/ML PROTEIN, 20% PEG1000, 0.1M IMIDAZOLE PH 8.0, 0.2 M CAAC2
Crystal Properties
Matthews coefficientSolvent content
2.2745.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.115α = 90
b = 67.992β = 90.11
c = 77.186γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
11.946.1393.50.073335312

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1G9Z1.946.1333531176193.50.1450.1410.223RANDOM32.65
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]
-0.250.150.070.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.329
r_dihedral_angle_4_deg22.695
r_dihedral_angle_3_deg16.884
r_dihedral_angle_1_deg8.591
r_scangle_it8.047
r_scbond_it6.628
r_mcangle_it4.651
r_mcbond_it3.267
r_angle_refined_deg2.059
r_xyhbond_nbd_refined0.367
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.329
r_dihedral_angle_4_deg22.695
r_dihedral_angle_3_deg16.884
r_dihedral_angle_1_deg8.591
r_scangle_it8.047
r_scbond_it6.628
r_mcangle_it4.651
r_mcbond_it3.267
r_angle_refined_deg2.059
r_xyhbond_nbd_refined0.367
r_symmetry_hbond_refined0.344
r_nbtor_refined0.322
r_nbd_refined0.283
r_symmetry_vdw_refined0.281
r_metal_ion_refined0.209
r_chiral_restr0.14
r_bond_refined_d0.013
r_gen_planes_refined0.009
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_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2461
Nucleic Acid Atoms979
Solvent Atoms348
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing