9SD6 | pdb_00009sd6

Crystal structure of the C-terminally truncated human E430Q/E574Q-PGGHG double mutant in complex with kojibiose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.35289Ratio: 1:1 Conditions: 25% PEG 3350, 0.1 M Bis-Tris-propane pH 7.35 and 0.2 M NaCl Soaking for 2 hours with 10 mM KJB
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.005α = 90
b = 77.169β = 99.249
c = 79.055γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-02-05MSINGLE 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
11.778.0399.80.0620.993610.36.57028721.2
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)
11.71.731000.4440.551.86.9

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 REPLACEMENTTHROUGHOUT1.754.92870264343999.7520.1940.19310.20150.21140.2166RANDOM21.583
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]
-0.261-0.04-0.0680.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.105
r_dihedral_angle_3_deg12.596
r_dihedral_angle_1_deg6.943
r_dihedral_angle_2_deg5.823
r_lrange_it4.985
r_lrange_other4.985
r_scangle_it2.817
r_scangle_other2.817
r_mcangle_it2.169
r_mcangle_other2.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.105
r_dihedral_angle_3_deg12.596
r_dihedral_angle_1_deg6.943
r_dihedral_angle_2_deg5.823
r_lrange_it4.985
r_lrange_other4.985
r_scangle_it2.817
r_scangle_other2.817
r_mcangle_it2.169
r_mcangle_other2.168
r_scbond_it1.72
r_scbond_other1.719
r_mcbond_it1.35
r_mcbond_other1.349
r_angle_refined_deg1.348
r_angle_other_deg0.479
r_nbd_refined0.202
r_symmetry_nbd_other0.194
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.17
r_symmetry_xyhbond_nbd_refined0.17
r_symmetry_nbd_refined0.166
r_nbd_other0.155
r_symmetry_nbtor_other0.08
r_chiral_restr0.068
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5322
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
MOLREPphasing
Cootmodel building
autoPROCdata reduction
Aimlessdata scaling