2VLD

crystal structure of a repair endonuclease from Pyrococcus abyssi


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7
Crystal Properties
Matthews coefficientSolvent content
2.7655

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.966α = 90
b = 100.688β = 90
c = 157.686γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.625990.0537.34.6196392
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)
12.62.799.40.412.93

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 DIFFRACTIONMADTHROUGHOUTNONE2.6101830699699.90.2430.2430.248RANDOM66.65
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]
8.38-5.97-2.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.815
r_dihedral_angle_4_deg21.369
r_dihedral_angle_3_deg20.302
r_dihedral_angle_1_deg7.896
r_scangle_it3.889
r_scbond_it2.431
r_mcangle_it1.963
r_angle_refined_deg1.462
r_mcbond_it1.2
r_symmetry_vdw_refined0.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.815
r_dihedral_angle_4_deg21.369
r_dihedral_angle_3_deg20.302
r_dihedral_angle_1_deg7.896
r_scangle_it3.889
r_scbond_it2.431
r_mcangle_it1.963
r_angle_refined_deg1.462
r_mcbond_it1.2
r_symmetry_vdw_refined0.399
r_nbtor_refined0.313
r_symmetry_hbond_refined0.244
r_nbd_refined0.231
r_xyhbond_nbd_refined0.145
r_chiral_restr0.099
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_refined
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 Atoms3679
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing