3AGO

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RTUPDB ENTRY 1RTU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.7529312.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.646425.2916

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.586α = 90
b = 39.425β = 108.98
c = 31.646γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 4r2010-01-01MSINGLE 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
10.9934.396.20.061589.2430539.8
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)
10.991.0292.40.4336.66.73011

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 1RTU0.9932.7140857219696.040.1510.150.162RANDOM9.168
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]
0.520.14-10.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg17.894
r_dihedral_angle_3_deg11.827
r_dihedral_angle_1_deg7.373
r_scangle_it4.03
r_angle_other_deg3.524
r_scbond_it2.848
r_mcangle_it2.166
r_angle_refined_deg1.9
r_mcbond_it1.411
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg17.894
r_dihedral_angle_3_deg11.827
r_dihedral_angle_1_deg7.373
r_scangle_it4.03
r_angle_other_deg3.524
r_scbond_it2.848
r_mcangle_it2.166
r_angle_refined_deg1.9
r_mcbond_it1.411
r_rigid_bond_restr1.118
r_mcbond_other0.412
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms870
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms26

Software

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