3D5G

Structure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229830% ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.9458.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.655α = 90
b = 67.667β = 100.63
c = 57.085γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X311.1EMBL/DESY, HAMBURGX31

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
11.81297.70.03732.1634199341992124.34
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)
1.81.8274.70.24

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1PYL1.811.9823239332393171397.450.17710.173660.24323RANDOM22.318
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]
-0.450.251.46-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.464
r_dihedral_angle_4_deg19.485
r_dihedral_angle_3_deg16.117
r_sphericity_free9.982
r_dihedral_angle_1_deg7.176
r_scangle_it4.954
r_sphericity_bonded4.315
r_scbond_it3.684
r_mcangle_it2.739
r_rigid_bond_restr2.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.464
r_dihedral_angle_4_deg19.485
r_dihedral_angle_3_deg16.117
r_sphericity_free9.982
r_dihedral_angle_1_deg7.176
r_scangle_it4.954
r_sphericity_bonded4.315
r_scbond_it3.684
r_mcangle_it2.739
r_rigid_bond_restr2.618
r_mcbond_it2.203
r_angle_refined_deg1.892
r_angle_other_deg1.554
r_mcbond_other0.777
r_symmetry_vdw_refined0.309
r_xyhbond_nbd_other0.307
r_symmetry_hbond_refined0.259
r_symmetry_vdw_other0.255
r_xyhbond_nbd_refined0.244
r_nbd_refined0.231
r_nbd_other0.231
r_nbtor_refined0.192
r_chiral_restr0.112
r_nbtor_other0.092
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2307
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing