7Q9R

Cocrystal structure of PDE6D bound to NRAS peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TB5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2790.1 M citric acid pH 4.0 and 3.2 M AmSO4
Crystal Properties
Matthews coefficientSolvent content
3.0259.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.788α = 90
b = 55.788β = 90
c = 114.842γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.5114.871000.99510.59.57634
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.560.859

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-VALUE5TB52.548.36760234699.9740.2350.23350.275928.585
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]
0.7310.3660.731-2.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg17.789
r_dihedral_angle_3_deg15.165
r_dihedral_angle_1_deg6.695
r_lrange_it2.696
r_lrange_other2.687
r_mcangle_it1.169
r_mcangle_other1.168
r_angle_refined_deg1.016
r_angle_other_deg0.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg17.789
r_dihedral_angle_3_deg15.165
r_dihedral_angle_1_deg6.695
r_lrange_it2.696
r_lrange_other2.687
r_mcangle_it1.169
r_mcangle_other1.168
r_angle_refined_deg1.016
r_angle_other_deg0.997
r_scangle_it0.668
r_scangle_other0.668
r_mcbond_it0.618
r_mcbond_other0.618
r_scbond_it0.327
r_scbond_other0.325
r_nbd_other0.285
r_symmetry_nbd_other0.223
r_symmetry_nbd_refined0.202
r_nbd_refined0.201
r_xyhbond_nbd_refined0.19
r_nbtor_refined0.16
r_symmetry_xyhbond_nbd_refined0.096
r_symmetry_xyhbond_nbd_other0.081
r_symmetry_nbtor_other0.07
r_chiral_restr0.019
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1197
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing