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Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with gluconolactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AZX PDB ENTRY 3AZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 41-46% (w/v) polypropylenglycol P400, 0.05-0.2M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.99 α = 90 b = 120.232 β = 90 c = 120.995 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r Vertically Collimating Premirror, Toroidal Focusing Mirror 2010-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.81 30 99.6 0.06 29.2 6.6 144332 140042 1 41.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.89 99.9 0.576 3.2 6.8 13952
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AZX 1.81 26.4 139710 7013 98.98 0.17126 0.16974 0.1789 0.20018 0.189 RANDOM 30.18
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] -1.19 1.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.967 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_3_deg 12.079 r_dihedral_angle_1_deg 6.992 r_scangle_it 5.06 r_scbond_it 3.393 r_mcangle_it 2.225 r_rigid_bond_restr 1.784 r_angle_refined_deg 1.415 r_mcbond_it 1.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.967 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_3_deg 12.079 r_dihedral_angle_1_deg 6.992 r_scangle_it 5.06 r_scbond_it 3.393 r_mcangle_it 2.225 r_rigid_bond_restr 1.784 r_angle_refined_deg 1.415 r_mcbond_it 1.339 r_chiral_restr 0.099 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 8100 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling