1PYL

Crystal structure of Ribonuclease Sa2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RGGPDB ENTRY 1RGG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.98α = 90
b = 34.13β = 109.5
c = 72.27γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKUMIRRORS1997-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.52598.60.06322.33.5306433064324.4
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)
1.51.5590.20.2722.651894

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1RGG1.507252966897598.140.150.150090.149330.1723RANDOM22.179
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]
-0.55-0.440.9-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.982
r_dihedral_angle_1_deg6.464
r_scangle_it5.178
r_sphericity_bonded4.639
r_scbond_it3.507
r_mcangle_it2.653
r_angle_other_deg1.745
r_mcbond_it1.613
r_rigid_bond_restr1.58
r_angle_refined_deg1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.982
r_dihedral_angle_1_deg6.464
r_scangle_it5.178
r_sphericity_bonded4.639
r_scbond_it3.507
r_mcangle_it2.653
r_angle_other_deg1.745
r_mcbond_it1.613
r_rigid_bond_restr1.58
r_angle_refined_deg1.54
r_nbd_refined0.299
r_symmetry_vdw_other0.259
r_nbd_other0.257
r_xyhbond_nbd_refined0.203
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.153
r_nbtor_other0.134
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3024
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing