4ZEN

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529316-18% PEG 8K, 0.1 M imidazole pH 6.5, 3% MPD
Crystal Properties
Matthews coefficientSolvent content
2.4950.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.517α = 90
b = 68.674β = 99.03
c = 153.281γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2014-01-01MSINGLE 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
11.935097.10.07816.5383233
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)
11.931.9679.10.3162.11.9

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 REPLACEMENTTHROUGHOUT4ZEH1.9326.2272157383191.30.159030.156760.20187RANDOM38.974
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]
2.561.03-1.47-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.734
r_dihedral_angle_4_deg19.054
r_dihedral_angle_3_deg13.44
r_long_range_B_refined7.508
r_long_range_B_other7.508
r_dihedral_angle_1_deg6.416
r_scangle_other5.975
r_scbond_it4.229
r_scbond_other4.228
r_mcangle_it4.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.734
r_dihedral_angle_4_deg19.054
r_dihedral_angle_3_deg13.44
r_long_range_B_refined7.508
r_long_range_B_other7.508
r_dihedral_angle_1_deg6.416
r_scangle_other5.975
r_scbond_it4.229
r_scbond_other4.228
r_mcangle_it4.172
r_mcangle_other4.172
r_mcbond_it3.324
r_mcbond_other3.322
r_angle_refined_deg1.815
r_angle_other_deg0.923
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms486
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing