2R2Q

Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GNUPDB entry 1GNU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529125% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.141.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.86α = 111.09
b = 38.193β = 95.91
c = 45.746γ = 108.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-08-10MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS2007-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418
2ROTATING ANODERIGAKU FR-E+ DW1.5418

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
1,21.653094.90.04227.53.524587
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)
1.651.71650.0822.21689

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 1GNU1.6518.52455191095.0450.2010.2010.20.234thin shells16.9
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]
0.432-0.07-1.123-0.474-0.43-0.542
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.967
r_dihedral_angle_4_deg18.266
r_dihedral_angle_3_deg13.147
r_dihedral_angle_1_deg6.018
r_scangle_it3.805
r_mcangle_it3.482
r_scbond_it2.81
r_mcbond_it2.689
r_angle_refined_deg1.449
r_angle_other_deg0.902
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.967
r_dihedral_angle_4_deg18.266
r_dihedral_angle_3_deg13.147
r_dihedral_angle_1_deg6.018
r_scangle_it3.805
r_mcangle_it3.482
r_scbond_it2.81
r_mcbond_it2.689
r_angle_refined_deg1.449
r_angle_other_deg0.902
r_mcbond_other0.787
r_symmetry_vdw_other0.283
r_nbd_refined0.213
r_nbd_other0.195
r_nbtor_refined0.186
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.121
r_chiral_restr0.093
r_nbtor_other0.082
r_symmetry_vdw_refined0.079
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1905
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms3

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction