2XNZ

xpt-pbuX C74U Riboswitch from B. subtilis bound to acetoguanamine identified by virtual screening


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G9CPDB ENTRY 2G9C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510MM K-HEPES PH 7.5, 12MM COBALT HEXAMMINE, 800MM AMMONIUM ACETATE, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2545.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.165α = 90
b = 35.068β = 90.06
c = 41.798γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.666.0898.50.0430.23.725334
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)
11.61.6698.10.42.9

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 ENTRY 2G9C1.5966.0823956128097.530.199680.197830.23424RANDOM25.438
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]
0.870.11-0.59-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.806
r_angle_refined_deg1.546
r_scbond_it1.271
r_mcangle_it1.135
r_mcbond_it0.744
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.806
r_angle_refined_deg1.546
r_scbond_it1.271
r_mcangle_it1.135
r_mcbond_it0.744
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1382
Solvent Atoms216
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing