1Y27 | pdb_00001y27

G-riboswitch-guanine complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y26PDB ENTRY 1Y26

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277Mg, PEG, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.632α = 90
b = 50.878β = 90
c = 217.439γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.14NSLSX25

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
12.42010.0927.792781
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)
12.42.4910.4568

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Y262.4201879145097.60.2330.2320.240.2640.27RANDOM51.3
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]
0.83.75-4.55
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg2.477
r_scangle_it1.069
r_scbond_it0.662
r_nbtor_refined0.27
r_nbd_refined0.192
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.118
r_chiral_restr0.063
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1456
Solvent Atoms18
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data scaling
CCP4phasing