3AZY

Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8


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
3.1160.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.42α = 90
b = 120.42β = 90
c = 107.195γ = 90
Symmetry
Space GroupP 43

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
11.653099.80.05726.85.6183497183216133.4
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)
11.651.711000.4413.25.618166

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 3AZX1.6524.6183046919799.780.164360.162880.19226RANDOM22.41
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]
0.610.61-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg12.747
r_dihedral_angle_3_deg11.667
r_dihedral_angle_1_deg7.121
r_scangle_it4.545
r_scbond_it3.09
r_mcangle_it2.045
r_rigid_bond_restr1.515
r_angle_refined_deg1.422
r_mcbond_it1.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg12.747
r_dihedral_angle_3_deg11.667
r_dihedral_angle_1_deg7.121
r_scangle_it4.545
r_scbond_it3.09
r_mcangle_it2.045
r_rigid_bond_restr1.515
r_angle_refined_deg1.422
r_mcbond_it1.239
r_chiral_restr0.104
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 Atoms8132
Nucleic Acid Atoms
Solvent Atoms809
Heterogen Atoms64

Software

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