3RL9

Crystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AHAPDB ENTRY 1AHA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG 6000, 0.1M Sodium Phosphate , pH 6.7 , VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.019α = 90
b = 130.019β = 90
c = 39.62γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2010-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.96599.90.10115.4186591865923.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9599.20.6284.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1AHA1.9291865918659100699.970.199980.197940.23778RANDOM30.719
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]
-2.21-1.1-2.213.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.428
r_dihedral_angle_4_deg13.709
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg4.483
r_scangle_it1.221
r_angle_refined_deg0.865
r_scbond_it0.694
r_mcangle_it0.499
r_mcbond_it0.262
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.428
r_dihedral_angle_4_deg13.709
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg4.483
r_scangle_it1.221
r_angle_refined_deg0.865
r_scbond_it0.694
r_mcangle_it0.499
r_mcbond_it0.262
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms30

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling