1RTU

USTILAGO SPHAEROGENA RIBONUCLEASE U2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RNTRNASE T1 (PDB ENTRY 1RNT)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM SULFATE, EQUILIBRATED AGAINST A RESERVOIR OF 0.9M AMMONIUM SULFATE CONTAINING 0.1M ACETATE BUFFER (PH 4.5)., vapor diffusion - hanging drop
Crystal Properties
Matthews coefficientSolvent content
2.1342.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.32α = 90
b = 61.27β = 90
c = 34.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray284IMAGE PLATEFUJIDOUBLE FOCUSSING MIRROR1990-05-22M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORYPhoton Factory

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
11.81296.10.0342499031
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)
11.81.8786.40.0773

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTRNASE T1 (PDB ENTRY 1RNT)1.889807980796.50.14313.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor25.2
p_staggered_tor12.4
p_scangle_it2.72
p_planar_tor2.6
p_scbond_it1.73
p_mcangle_it1.214
p_mcbond_it0.76
p_xyhbond_nbd0.173
p_chiral_restr0.17
p_singtor_nbd0.157
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor25.2
p_staggered_tor12.4
p_scangle_it2.72
p_planar_tor2.6
p_scbond_it1.73
p_mcangle_it1.214
p_mcbond_it0.76
p_xyhbond_nbd0.173
p_chiral_restr0.17
p_singtor_nbd0.157
p_multtor_nbd0.147
p_planar_d0.041
p_angle_d0.028
p_bond_d0.014
p_plane_restr0.014
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms870
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms5

Software

Software
Software NamePurpose
OSCMGRdata collection
TOMOKOdata reduction
MARIKOdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
OSCdata reduction
Adata scaling
MARIKOdata scaling
X-PLORphasing