1U8X | pdb_00001u8x

CRYSTAL STRUCTURE OF GLVA FROM BACILLUS SUBTILIS, A METAL-REQUIRING, NAD-DEPENDENT 6-PHOSPHO-ALPHA-GLUCOSIDASE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherSAD, AUTO BUILT MODEL FROM RESOLVE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82950.2M MgCl2, 0.1M Tris-Cl, pH8.0, 28% PEG4000, 10% (v/v)glycerol, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.858.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.604α = 90
b = 102.017β = 90
c = 144.748γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.4CCDMARRESEARCH2002-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B0.979APS5ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.053099.80.10211.37.527516038535
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)
12.052.199.90.5697.52536

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTAUTO-BUILT MODEL FROM RESOLVE2.0530.0233021330213655950.1970.1970.1950.210.2210.22RANDOM28.91
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]
-2.733.16-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.834
r_scangle_it3.576
r_scbond_it2.194
r_mcangle_it1.406
r_angle_refined_deg1.332
r_angle_other_deg0.832
r_mcbond_it0.743
r_symmetry_hbond_refined0.421
r_symmetry_vdw_other0.285
r_nbd_other0.239
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3449
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms61

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement