1TDZ

Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NNJPDB ENTRY 1NNJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293hepes, sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3763.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.408α = 90
b = 91.408β = 90
c = 141.575γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.9330ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.876.799.30.0488.73.6557815578124.879
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.2343.13.68083

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NNJ1.8205284452844282599.070.180340.180340.178910.20697RANDOM28.788
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]
-0.02-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.737
r_scangle_it4.122
r_scbond_it2.62
r_mcangle_it1.755
r_angle_refined_deg1.709
r_mcbond_it0.989
r_nbd_refined0.21
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.737
r_scangle_it4.122
r_scbond_it2.62
r_mcangle_it1.755
r_angle_refined_deg1.709
r_mcbond_it0.989
r_nbd_refined0.21
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.131
r_chiral_restr0.109
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2110
Nucleic Acid Atoms569
Solvent Atoms431
Heterogen Atoms7

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling