5TEF

Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TEEapo GEMIN5 WD40 repeats

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529315% PEG4000, 0.2 M ammonium acetate, 0.1 sodium citrate, 0.0005-0.001 M m7GpppG
Crystal Properties
Matthews coefficientSolvent content
2.3547.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.658α = 90
b = 124.862β = 117.52
c = 60.938γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97944APS23-ID-B

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
11.9548.0298.60.0790.0920.0460.997113.955703
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)
11.95297.60.6750.7810.3930.8471.83.93879

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT"apo" GEMIN5 WD40 repeats1.9548.0252871280298.40.18070.17870.217434.097
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]
1.14-0.71-3.161.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.285
r_dihedral_angle_4_deg13.895
r_dihedral_angle_3_deg12.8
r_dihedral_angle_1_deg6.914
r_mcangle_it4.677
r_mcbond_it3.317
r_mcbond_other3.317
r_angle_refined_deg1.524
r_angle_other_deg0.943
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.285
r_dihedral_angle_4_deg13.895
r_dihedral_angle_3_deg12.8
r_dihedral_angle_1_deg6.914
r_mcangle_it4.677
r_mcbond_it3.317
r_mcbond_other3.317
r_angle_refined_deg1.524
r_angle_other_deg0.943
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5186
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing