7QPW

X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.129822 % PEG 4K 0.01 M sodium citrate pH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.2244.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.5α = 90
b = 32.91β = 90.164
c = 73.06γ = 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
11.1573.0699.60.0780.0510.99710.36.184723
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)
11.151.171000.6990.4790.7382.25.4

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-VALUE1JVT1.1573.0684723415699.60.1370.1360.165417.985
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]
-0.7710.5080.2680.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_3_deg12.296
r_dihedral_angle_4_deg11.199
r_rigid_bond_restr7.571
r_dihedral_angle_1_deg7.34
r_lrange_it6.318
r_lrange_other5.841
r_scangle_it5.537
r_scangle_other5.537
r_scbond_it4.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_3_deg12.296
r_dihedral_angle_4_deg11.199
r_rigid_bond_restr7.571
r_dihedral_angle_1_deg7.34
r_lrange_it6.318
r_lrange_other5.841
r_scangle_it5.537
r_scangle_other5.537
r_scbond_it4.735
r_scbond_other4.731
r_mcangle_it4.315
r_mcangle_other4.313
r_mcbond_other4.3
r_mcbond_it4.298
r_angle_refined_deg3.404
r_angle_other_deg1.659
r_nbd_refined0.285
r_nbd_other0.23
r_symmetry_nbd_other0.214
r_symmetry_nbd_refined0.206
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.167
r_chiral_restr0.11
r_symmetry_nbtor_other0.09
r_bond_refined_d0.018
r_symmetry_xyhbond_nbd_other0.016
r_gen_planes_refined0.014
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1881
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing