3RGG

Crystal structure of Treponema denticola PurE bound to AIR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative coordinate

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829814-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.39α = 90
b = 155.13β = 90
c = 88.14γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray111IMAGE PLATERIGAKU RAXIS IV2006-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
11.8237.198.60.064206.45125751257
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)
11.821.8792.30.8652.25.13520

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNative coordinate1.8237.14851048510260798.340.189850.188160.22155RANDOM28.749
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]
-0.842.22-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.951
r_dihedral_angle_3_deg14.381
r_dihedral_angle_4_deg12.906
r_dihedral_angle_1_deg5.792
r_scangle_it3.362
r_scbond_it2.183
r_angle_refined_deg1.674
r_mcangle_it1.212
r_angle_other_deg0.98
r_mcbond_it0.731
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.951
r_dihedral_angle_3_deg14.381
r_dihedral_angle_4_deg12.906
r_dihedral_angle_1_deg5.792
r_scangle_it3.362
r_scbond_it2.183
r_angle_refined_deg1.674
r_mcangle_it1.212
r_angle_other_deg0.98
r_mcbond_it0.731
r_mcbond_other0.216
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4703
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms76

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling