7QPY

X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (3)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.129822 % PEG 4K 0.01 M sodium citrate pH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.1743.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.22α = 90
b = 32.5β = 90.408
c = 72.38γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.00ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4250.11599.10.0760.050.99612.7644454
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.4499.10.5230.4060.792.34.4

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE!JVT1.4250.11544171231499.1920.1790.17670.212220.709
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]
-0.0260.066-0.0050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_3_deg12.559
r_dihedral_angle_4_deg12.123
r_dihedral_angle_1_deg7.158
r_lrange_other6.816
r_lrange_it6.813
r_scangle_it4.112
r_scangle_other4.018
r_angle_refined_deg3.69
r_mcangle_it3.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_3_deg12.559
r_dihedral_angle_4_deg12.123
r_dihedral_angle_1_deg7.158
r_lrange_other6.816
r_lrange_it6.813
r_scangle_it4.112
r_scangle_other4.018
r_angle_refined_deg3.69
r_mcangle_it3.414
r_mcangle_other3.413
r_scbond_it2.686
r_scbond_other2.678
r_mcbond_it2.196
r_mcbond_other2.196
r_angle_other_deg1.54
r_nbd_refined0.201
r_symmetry_xyhbond_nbd_refined0.201
r_symmetry_nbd_other0.191
r_symmetry_nbd_refined0.185
r_nbd_other0.18
r_xyhbond_nbd_refined0.175
r_nbtor_refined0.17
r_chiral_restr0.088
r_symmetry_nbtor_other0.086
r_xyhbond_nbd_other0.066
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1878
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing