4ZEP

Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZE4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529316-18% PEG 8K, 3% MPD, 0.1M imidazole buffer pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4750.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.158α = 90
b = 68.944β = 100.39
c = 152.896γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.215099.50.08511.43.955496
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)
12.212.2594.70.3013.33.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4ZE42.2128.3152090278898.890.153540.150680.20703RANDOM34.236
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]
3.440.85-1.68-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.423
r_dihedral_angle_4_deg17.604
r_dihedral_angle_3_deg14.422
r_long_range_B_refined7.009
r_long_range_B_other7.008
r_dihedral_angle_1_deg6.698
r_scangle_other5.54
r_mcangle_it3.874
r_mcangle_other3.873
r_scbond_it3.652
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.423
r_dihedral_angle_4_deg17.604
r_dihedral_angle_3_deg14.422
r_long_range_B_refined7.009
r_long_range_B_other7.008
r_dihedral_angle_1_deg6.698
r_scangle_other5.54
r_mcangle_it3.874
r_mcangle_other3.873
r_scbond_it3.652
r_scbond_other3.652
r_mcbond_it2.775
r_mcbond_other2.775
r_angle_refined_deg1.799
r_angle_other_deg0.914
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7748
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing