2GAO

Crystal Structure of Human SAR1a in Complex With GDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29130% PEG8000, 0.2M ammonium sulfate, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.295α = 90
b = 63.814β = 105.94
c = 62.132γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
123099.90.19954.329052
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0799.24

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB Entry: 1F6B23029010147099.2270.2260.22380.2694thin shells18.669
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]
0.9140.138-1.3760.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.112
r_dihedral_angle_4_deg18.716
r_dihedral_angle_3_deg12.564
r_dihedral_angle_1_deg4.935
r_mcangle_it3.217
r_scangle_it3.019
r_mcbond_it2.71
r_scbond_it2.218
r_angle_refined_deg1.422
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.112
r_dihedral_angle_4_deg18.716
r_dihedral_angle_3_deg12.564
r_dihedral_angle_1_deg4.935
r_mcangle_it3.217
r_scangle_it3.019
r_mcbond_it2.71
r_scbond_it2.218
r_angle_refined_deg1.422
r_angle_other_deg0.953
r_mcbond_other0.605
r_symmetry_vdw_refined0.261
r_symmetry_vdw_other0.205
r_nbd_refined0.2
r_nbd_other0.187
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.156
r_chiral_restr0.083
r_nbtor_other0.082
r_symmetry_hbond_refined0.066
r_bond_refined_d0.017
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2661
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms58

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction