3B01

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 3AZYPDB ENTRY 3AZY

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
3.160.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.305α = 90
b = 120.305β = 90
c = 107.154γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertically Focusing Mirror2010-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97622NSRRCBL13C1

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
11.873099.70.06527.46.2125924125562139
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)
11.871.941000.5173.96.112561

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 3AZY1.8727.5125430629899.630.153480.15170.18771RANDOM28.415
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]
0.180.18-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg13.339
r_dihedral_angle_3_deg12.658
r_dihedral_angle_1_deg6.994
r_scangle_it5.128
r_scbond_it3.378
r_mcangle_it2.289
r_rigid_bond_restr1.768
r_angle_refined_deg1.406
r_mcbond_it1.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg13.339
r_dihedral_angle_3_deg12.658
r_dihedral_angle_1_deg6.994
r_scangle_it5.128
r_scbond_it3.378
r_mcangle_it2.289
r_rigid_bond_restr1.768
r_angle_refined_deg1.406
r_mcbond_it1.348
r_chiral_restr0.101
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms8123
Nucleic Acid Atoms
Solvent Atoms664
Heterogen Atoms47

Software

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