3QWM | pdb_00003qwm

Crystal Structure of GEP100, the plextrin homology domain of IQ motif and SEC7 domain-containing protein 1 isoform a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2527717.5%(w/v) PEG 3350, 0.20M Na nitrate, 10.0%(v/v) ethylene glycol, 0.1M Bis-Tris propane, pH 8.25, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3162.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.73α = 90
b = 56.73β = 90
c = 234.08γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-01-28MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152010-04-29MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03
2SYNCHROTRONDIAMOND BEAMLINE I040.984DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1,22.3948.0799.80.08810.65.496589658-3-372.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.392.5299.90.66723.51343

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT2.3948.079587958748799.670.243690.243690.242280.240.272420.27RANDOM59.584
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]
0.50.250.5-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.685
r_dihedral_angle_4_deg18.157
r_dihedral_angle_3_deg17.601
r_dihedral_angle_1_deg5.854
r_angle_refined_deg1.288
r_angle_other_deg0.772
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.685
r_dihedral_angle_4_deg18.157
r_dihedral_angle_3_deg17.601
r_dihedral_angle_1_deg5.854
r_angle_refined_deg1.288
r_angle_other_deg0.772
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1035
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms

Software

Software
Software NamePurpose
GDAdata collection
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling