2G6V

The crystal structure of ribD from Escherichia coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293In 500uL reservoir: 0.1M MES, 3% (v/v) 1,6 Hexandiol, 2+2uL drops , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.8768.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.6α = 90
b = 172.6β = 90
c = 76.38γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.628.2586.840482-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7100

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 DIFFRACTIONSADTHROUGHOUT2.628.2540426201099.960.246260.246260.244220.28544RANDOM87.154
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]
0.340.170.34-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.282
r_dihedral_angle_3_deg19.913
r_dihedral_angle_4_deg19.057
r_dihedral_angle_1_deg6.517
r_scangle_it2.113
r_angle_refined_deg1.327
r_scbond_it1.323
r_mcangle_it0.882
r_mcbond_it0.534
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.282
r_dihedral_angle_3_deg19.913
r_dihedral_angle_4_deg19.057
r_dihedral_angle_1_deg6.517
r_scangle_it2.113
r_angle_refined_deg1.327
r_scbond_it1.323
r_mcangle_it0.882
r_mcbond_it0.534
r_nbtor_refined0.306
r_nbd_refined0.239
r_symmetry_vdw_refined0.236
r_xyhbond_nbd_refined0.208
r_chiral_restr0.088
r_symmetry_hbond_refined0.056
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5465
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SOLVEphasing