8HBA

Crystal structure of NAD-II riboswitch (single strand) with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8HB1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.012 M Sodium chloride, 0.08 M Potassium chloride 0.04 M Sodium cacodylate trihydrate pH 5.5 45% v/v (+/-)-2-Methyl-2,4-pentanediol 0.02 M Hexammine cobalt(III) chloride
Crystal Properties
Matthews coefficientSolvent content
2.1643.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.756α = 90
b = 68.64β = 90
c = 114.009γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.6419.6199.20.0520.0160.91923.311.9991352
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.642.7494.30.8970.2920.9192

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 REPLACEMENTTHROUGHOUT8HB12.6419.61816893498.890.23390.22940.27456RANDOM103.385
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]
10.64-4.23-6.41
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.374
r_long_range_B_other9.374
r_scangle_other4.045
r_scbond_it2.5
r_scbond_other2.5
r_angle_refined_deg1.749
r_angle_other_deg1.677
r_chiral_restr0.104
r_gen_planes_refined0.012
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.374
r_long_range_B_other9.374
r_scangle_other4.045
r_scbond_it2.5
r_scbond_other2.5
r_angle_refined_deg1.749
r_angle_other_deg1.677
r_chiral_restr0.104
r_gen_planes_refined0.012
r_bond_refined_d0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2111
Solvent Atoms
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing