5GXI

Structure of the Gemin5 WD40 domain in complex with AAUUUUUGAG


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
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.85α = 90
b = 124.52β = 116.77
c = 60.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS II2016-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
11.8528.9299.90.99814.97.365191
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)
11.851.999.90.5921.87

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,3DM01.8528.961867329499.930.166140.163950.20738RANDOM24.115
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_deg31.108
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg12.916
r_dihedral_angle_1_deg7.187
r_long_range_B_refined6.239
r_long_range_B_other6.163
r_scangle_other4.308
r_mcangle_it3.504
r_mcangle_other3.504
r_scbond_it2.943
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.108
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg12.916
r_dihedral_angle_1_deg7.187
r_long_range_B_refined6.239
r_long_range_B_other6.163
r_scangle_other4.308
r_mcangle_it3.504
r_mcangle_other3.504
r_scbond_it2.943
r_scbond_other2.942
r_mcbond_it2.407
r_mcbond_other2.402
r_angle_refined_deg1.894
r_angle_other_deg1.062
r_chiral_restr0.119
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 Atoms5150
Nucleic Acid Atoms82
Solvent Atoms381
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing