1XC8

CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TDZPDB ENTRY 1TDZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7303HEPES, SODIUM CITRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
3.5264.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.513α = 90
b = 92.513β = 90
c = 142.867γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.92004ESRFBM30A

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
11.9517.24791.40.0697.74580641650
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)
11.952.0691.40.2842.64.86134

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 1TDZ1.9517.2473956139561208990.870.178050.178050.17640.20932RANDOM35.412
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]
0.330.33-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.416
r_dihedral_angle_4_deg17.948
r_dihedral_angle_3_deg11.965
r_dihedral_angle_1_deg5.971
r_scangle_it3.962
r_scbond_it2.727
r_angle_refined_deg1.776
r_mcangle_it1.745
r_mcbond_it1.223
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.416
r_dihedral_angle_4_deg17.948
r_dihedral_angle_3_deg11.965
r_dihedral_angle_1_deg5.971
r_scangle_it3.962
r_scbond_it2.727
r_angle_refined_deg1.776
r_mcangle_it1.745
r_mcbond_it1.223
r_nbtor_refined0.303
r_nbd_refined0.211
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.133
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2128
Nucleic Acid Atoms569
Solvent Atoms397
Heterogen Atoms7

Software

Software
Software NamePurpose
Xnemodata collection
SCALAdata scaling
AMoREphasing
REFMACrefinement
XNEMOdata reduction
CCP4data scaling