3AHW

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AGNPDB ENTRY 3AGN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop, vapor diffusion6.5293PEG 8000, pH 6.5, hanging drop, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.994α = 90
b = 35.94β = 103.42
c = 36.151γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 4r2010-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.978Photon FactoryBL-6A

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
11.0337.999.20.09336.26.5482434787111.07
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)
1.031.05793.90.3952.233554

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 3AGN1.0325.1447871244599.230.1370.1370.144RANDOM10.729
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]
0.060.21-0.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_dihedral_angle_3_deg11.009
r_dihedral_angle_4_deg7.816
r_dihedral_angle_1_deg7.202
r_scangle_it4.455
r_scbond_it3.031
r_mcangle_it2.269
r_angle_refined_deg1.656
r_mcbond_it1.5
r_rigid_bond_restr1.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_dihedral_angle_3_deg11.009
r_dihedral_angle_4_deg7.816
r_dihedral_angle_1_deg7.202
r_scangle_it4.455
r_scbond_it3.031
r_mcangle_it2.269
r_angle_refined_deg1.656
r_mcbond_it1.5
r_rigid_bond_restr1.155
r_angle_other_deg0.927
r_mcbond_other0.461
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.008
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms870
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing