8PX0

Structure of ribonuclease A, solved at wavelength 2.75 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 mM sodium citrate pH 5.5, 28 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1643.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.98α = 90
b = 32.62β = 90.16
c = 72.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 12M2019-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I232.7552DiamondI23

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.850.0181.290.092910.095430.021080.99524.6717.517977
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.86465.040.34140.36440.120.9155.038.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.850.011707490381.340.202520.200630.23851RANDOM33.321
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]
-1.050.281.7-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg6.888
r_long_range_B_other6.246
r_long_range_B_refined6.244
r_dihedral_angle_2_deg5.848
r_scangle_other4.444
r_mcangle_it3.183
r_mcangle_other3.182
r_scbond_it3.012
r_scbond_other3.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg6.888
r_long_range_B_other6.246
r_long_range_B_refined6.244
r_dihedral_angle_2_deg5.848
r_scangle_other4.444
r_mcangle_it3.183
r_mcangle_other3.182
r_scbond_it3.012
r_scbond_other3.011
r_mcbond_it2.122
r_mcbond_other2.119
r_angle_refined_deg1.42
r_angle_other_deg0.467
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1875
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing