1JWF

Crystal Structure of human GGA1 VHS domain.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293PEG 3350, potassium dihydrogen phosphate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.12α = 90
b = 55.12β = 90
c = 105.513γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEFUJI2001-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6B1.0Photon FactoryBL-6B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.11595.6905739125
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1789.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1159057905745695.010.223370.223370.221540.26137RANDOM34.401
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]
-0.23-0.230.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.642
r_scangle_it5.275
r_scbond_it3.097
r_dihedral_angle_1_deg3.063
r_mcangle_it1.928
r_angle_refined_deg1.557
r_mcbond_it0.964
r_nbd_refined0.251
r_symmetry_vdw_refined0.251
r_xyhbond_nbd_refined0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.642
r_scangle_it5.275
r_scbond_it3.097
r_dihedral_angle_1_deg3.063
r_mcangle_it1.928
r_angle_refined_deg1.557
r_mcbond_it0.964
r_nbd_refined0.251
r_symmetry_vdw_refined0.251
r_xyhbond_nbd_refined0.19
r_symmetry_hbond_refined0.167
r_chiral_restr0.115
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1117
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement