3BF5

Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5277NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.45α = 90
b = 59.18β = 90
c = 177.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2007-10-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.91840, 0.97939, 0.97953APS23-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
11.9129.18598.40.0510.7846740-336.803
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)
11.911.9899.60.6851.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.9129.18546708236499.120.2050.2020.245RANDOM34.325
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]
2.390.3-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_4_deg14.311
r_dihedral_angle_3_deg12.183
r_scangle_it5.879
r_scbond_it4.387
r_dihedral_angle_1_deg3.758
r_mcangle_it2.42
r_mcbond_it1.636
r_angle_refined_deg1.596
r_angle_other_deg1.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_4_deg14.311
r_dihedral_angle_3_deg12.183
r_scangle_it5.879
r_scbond_it4.387
r_dihedral_angle_1_deg3.758
r_mcangle_it2.42
r_mcbond_it1.636
r_angle_refined_deg1.596
r_angle_other_deg1.272
r_mcbond_other0.45
r_nbd_refined0.167
r_nbtor_refined0.158
r_symmetry_vdw_other0.156
r_nbd_other0.136
r_symmetry_hbond_refined0.113
r_xyhbond_nbd_refined0.098
r_chiral_restr0.086
r_symmetry_vdw_refined0.081
r_nbtor_other0.072
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4352
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction