3QL1

Crystal Structure of Ribonuclease A Variant A4C/D83E/V118C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7RSA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M sodium acetate, 0.2 M ammonium sulfate, 25% (w/v) PEG 4000, 10mM copper chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.248α = 90
b = 53.781β = 117.95
c = 42.869γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.293590.60.05111.312753924943-318.017
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.291.32560.4290.552.06

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7RSA1.2932.24249432494312481000.15550.15550.15360.19RANDOM14.7261
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]
0.290.03-0.13-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.185
r_dihedral_angle_4_deg20.077
r_sphericity_free11.461
r_dihedral_angle_3_deg10.445
r_sphericity_bonded7.185
r_scangle_it7.032
r_dihedral_angle_1_deg6.096
r_scbond_it5.12
r_mcangle_it3.79
r_rigid_bond_restr2.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.185
r_dihedral_angle_4_deg20.077
r_sphericity_free11.461
r_dihedral_angle_3_deg10.445
r_sphericity_bonded7.185
r_scangle_it7.032
r_dihedral_angle_1_deg6.096
r_scbond_it5.12
r_mcangle_it3.79
r_rigid_bond_restr2.838
r_mcbond_it2.669
r_angle_refined_deg2.338
r_chiral_restr0.142
r_bond_refined_d0.025
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms952
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction