9NAD | pdb_00009nad

Human GSTO1-1 complexed with C5-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Reservoir volume consisted of 1 ml of 1.9 M (NH4)2SO4, 200 mM potassium sodium tartrate, 3.4 mM ZnSO4, 16.7 mM citric acid, 1.86 mM tri-sodium citrate. Protein (volume 1 uL) at 8.9 mg/ml in 20 mM Tris pH 8.0, 60 mM NaCl and 1 mM DTT was mixed with 1uL of reservoir solution on a siliconised cover slip.
Crystal Properties
Matthews coefficientSolvent content
2.4148.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.001α = 90
b = 57.001β = 90
c = 139.178γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9946.56898.90.0670.0830.0360.99810.85.218337
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0593.90.4820.5780.3460.9152.35.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.99446.5681831693698.5260.1870.1840.18720.24850.250434.526
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]
0.410.2050.41-1.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.782
r_dihedral_angle_6_deg14.175
r_lrange_it8.221
r_lrange_other8.171
r_dihedral_angle_1_deg6.219
r_dihedral_angle_2_deg5.804
r_scangle_other4.287
r_scangle_it4.284
r_scbond_it2.737
r_mcangle_it2.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.782
r_dihedral_angle_6_deg14.175
r_lrange_it8.221
r_lrange_other8.171
r_dihedral_angle_1_deg6.219
r_dihedral_angle_2_deg5.804
r_scangle_other4.287
r_scangle_it4.284
r_scbond_it2.737
r_mcangle_it2.736
r_mcangle_other2.735
r_scbond_other2.71
r_mcbond_it1.832
r_mcbond_other1.832
r_angle_refined_deg1.69
r_angle_other_deg0.61
r_nbd_refined0.243
r_nbd_other0.222
r_symmetry_nbd_other0.215
r_xyhbond_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.197
r_nbtor_refined0.194
r_symmetry_nbd_refined0.173
r_chiral_restr0.092
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.057
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1915
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing