3AZZ

Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with gluconolactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AZXPDB ENTRY 3AZX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829841-46% (w/v) polypropylenglycol P400, 0.05-0.2M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.99α = 90
b = 120.232β = 90
c = 120.995γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertically Collimating Premirror, Toroidal Focusing Mirror2010-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00000NSRRCBL13B1

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
11.813099.60.0629.26.6144332140042141.8
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)
11.821.8999.90.5763.26.813952

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3AZX1.8126.4139710701398.980.171260.169740.20018RANDOM30.18
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]
-1.191.060.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.967
r_dihedral_angle_4_deg15.382
r_dihedral_angle_3_deg12.079
r_dihedral_angle_1_deg6.992
r_scangle_it5.06
r_scbond_it3.393
r_mcangle_it2.225
r_rigid_bond_restr1.784
r_angle_refined_deg1.415
r_mcbond_it1.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.967
r_dihedral_angle_4_deg15.382
r_dihedral_angle_3_deg12.079
r_dihedral_angle_1_deg6.992
r_scangle_it5.06
r_scbond_it3.393
r_mcangle_it2.225
r_rigid_bond_restr1.784
r_angle_refined_deg1.415
r_mcbond_it1.339
r_chiral_restr0.099
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8100
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms80

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling