2EWR

Crystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP6.92770.2M KCl, 20.0% PEG-3350, No Buffer, pH 6.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1642.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.56α = 74.11
b = 36.21β = 86.38
c = 39.28γ = 79.69
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2005-08-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.95372, 0.97960, 0.97942APS23-ID-D

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
11.629.64388.80.02818.433.7520185
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)
11.61.6650.450.40.0956.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMADTHROUGHOUT1.629.6619130105590.080.1470.146580.1450.18RANDOM9.142
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]
-0.310.20.03-0.190.050.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.229
r_dihedral_angle_4_deg18.261
r_dihedral_angle_3_deg11.438
r_scangle_it6.283
r_dihedral_angle_1_deg5.902
r_scbond_it4.343
r_mcangle_it2.543
r_mcbond_it2.077
r_angle_refined_deg1.486
r_angle_other_deg0.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.229
r_dihedral_angle_4_deg18.261
r_dihedral_angle_3_deg11.438
r_scangle_it6.283
r_dihedral_angle_1_deg5.902
r_scbond_it4.343
r_mcangle_it2.543
r_mcbond_it2.077
r_angle_refined_deg1.486
r_angle_other_deg0.822
r_mcbond_other0.451
r_nbd_refined0.226
r_symmetry_vdw_other0.194
r_symmetry_hbond_refined0.191
r_nbd_other0.19
r_symmetry_vdw_refined0.186
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.153
r_chiral_restr0.093
r_nbtor_other0.082
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1284
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SOLVEphasing