6BCD

Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-RBM2 (residues 1988-2014)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ABD3ABD (excluding Rev3 peptide)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.25289.15well solution containing 100 mM sodium citrate, 1.6 M ammonium sulfate, pH=5.25 was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4
Crystal Properties
Matthews coefficientSolvent content
2.753.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.58α = 90
b = 64.58β = 90
c = 116.547γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray289.15PIXELDECTRIS PILATUS3 S 6M2016-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.976CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.43116.5598.50.0450.0480.01641.789.651936

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ABD (excluding Rev3 peptide)1.43116.5551936252198.490.1760.17490.1974RANDOM29.8026
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]
0.830.420.83-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.145
r_dihedral_angle_4_deg14.894
r_dihedral_angle_3_deg14.726
r_dihedral_angle_1_deg6.821
r_mcangle_it4.69
r_angle_other_deg3.679
r_mcbond_it3.255
r_mcbond_other3.255
r_angle_refined_deg2.367
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.145
r_dihedral_angle_4_deg14.894
r_dihedral_angle_3_deg14.726
r_dihedral_angle_1_deg6.821
r_mcangle_it4.69
r_angle_other_deg3.679
r_mcbond_it3.255
r_mcbond_other3.255
r_angle_refined_deg2.367
r_chiral_restr0.148
r_gen_planes_other0.027
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1856
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement