9SD5 | pdb_00009sd5

Crystal structure of the C-terminally truncated human E574Q-PGGHG mutant in complex with glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9SD4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.7289Ratio: 1:1 Co-crystallized with 10mM KJB Conditions: 20% PEG 3350, 0.1 M Tris pH 8.7, 0.2 M NaCl.
Crystal Properties
Matthews coefficientSolvent content
2.1743.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.071α = 90
b = 77.076β = 98.552
c = 79.888γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.367999.90.0270.99920.26.613792612.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.3999.90.2960.7573.45.6

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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.36379137898696599.9290.1370.13570.13570.15730.1573RANDOM14.084
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]
-0.240.374-0.3720.478
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.226
r_dihedral_angle_3_deg11.611
r_dihedral_angle_2_deg9.991
r_dihedral_angle_1_deg6.957
r_lrange_it5.763
r_lrange_other5.763
r_scangle_it4.256
r_scangle_other4.256
r_scbond_it2.869
r_scbond_other2.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.226
r_dihedral_angle_3_deg11.611
r_dihedral_angle_2_deg9.991
r_dihedral_angle_1_deg6.957
r_lrange_it5.763
r_lrange_other5.763
r_scangle_it4.256
r_scangle_other4.256
r_scbond_it2.869
r_scbond_other2.868
r_mcangle_it2.307
r_mcangle_other2.307
r_angle_refined_deg2.021
r_mcbond_it1.581
r_mcbond_other1.574
r_angle_other_deg0.69
r_symmetry_xyhbond_nbd_refined0.248
r_nbd_refined0.226
r_symmetry_nbd_refined0.219
r_nbd_other0.211
r_symmetry_nbd_other0.205
r_nbtor_refined0.189
r_xyhbond_nbd_refined0.173
r_chiral_restr0.108
r_symmetry_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5322
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms129

Software

Software
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building