5GXH

The structure of the Gemin5 WD40 domain with AAUUUUUG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OW83OW8,2HES,3DM0
experimental modelPDB 2HES3OW8,2HES,3DM0
experimental modelPDB 3DM03OW8,2HES,3DM0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.1 M sodium citrate, 0.2 M ammonium acetate, 15% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2645.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.138α = 90
b = 124.459β = 116.96
c = 60.808γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9791829APS19-ID

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
11.847.841000.99821.27.471182
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)
11.81.841000.752.37.5

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 REPLACEMENTTHROUGHOUT3OW8,2HES,3DM01.847.8467561358799.910.163480.161730.19656RANDOM24.693
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.313
r_dihedral_angle_4_deg16.108
r_dihedral_angle_3_deg12.627
r_dihedral_angle_1_deg6.956
r_long_range_B_refined6.553
r_long_range_B_other6.552
r_scangle_other4.725
r_mcangle_it3.65
r_mcangle_other3.65
r_scbond_it3.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.313
r_dihedral_angle_4_deg16.108
r_dihedral_angle_3_deg12.627
r_dihedral_angle_1_deg6.956
r_long_range_B_refined6.553
r_long_range_B_other6.552
r_scangle_other4.725
r_mcangle_it3.65
r_mcangle_other3.65
r_scbond_it3.225
r_scbond_other3.221
r_mcbond_it2.587
r_mcbond_other2.578
r_angle_refined_deg1.86
r_angle_other_deg1.071
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5144
Nucleic Acid Atoms127
Solvent Atoms317
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing