3IRH

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52950.2 M Sodium bromide, 0.1 M Bis-tris propane pH 7.5, 20 % w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1442.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.253α = 90
b = 188.66β = 90
c = 67.822γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBERYLLIUM LENSES/DIAMOND LAUE MONO2008-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
12.43099.10.08213.975951-3
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)
12.42.4995.30.552.41.9

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 ID 2O6I2.43071324378399.20.1880.1850.244RANDOM40.67
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]
-5.122.093.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg16.627
r_dihedral_angle_3_deg15.873
r_dihedral_angle_1_deg5.493
r_scangle_it3.06
r_scbond_it1.907
r_mcangle_it1.211
r_angle_refined_deg1.21
r_mcbond_it0.693
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg16.627
r_dihedral_angle_3_deg15.873
r_dihedral_angle_1_deg5.493
r_scangle_it3.06
r_scbond_it1.907
r_mcangle_it1.211
r_angle_refined_deg1.21
r_mcbond_it0.693
r_nbtor_refined0.304
r_metal_ion_refined0.245
r_nbd_refined0.204
r_symmetry_hbond_refined0.201
r_symmetry_vdw_refined0.197
r_xyhbond_nbd_refined0.154
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14635
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms188

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling