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Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HYK PDB ENTRY 2HYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 10-15% (w/v) PEG 8000, 0.25-0.45 M KH2PO4, 20% glycerol, 10mM CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.567 α = 90 b = 56.152 β = 105.26 c = 126.431 γ = 90
Symmetry Space Group C 1 2 1
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 2010-06-09 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 1.8 30 98.8 0.086 16.4 3.9 63060 62313 1 39.7
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 1.8 1.86 95.8 0.496 2.4 3.7 6270
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 2HYK 1.8 25.6 62297 3167 98.48 0.20052 0.19791 0.2116 0.24788 0.2601 RANDOM 27.051
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] -1.1 -0.3 1.78 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_1_deg 7.145 r_scangle_it 4.587 r_scbond_it 3.169 r_mcangle_it 1.983 r_rigid_bond_restr 1.63 r_angle_refined_deg 1.394 r_mcbond_it 1.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_1_deg 7.145 r_scangle_it 4.587 r_scbond_it 3.169 r_mcangle_it 1.983 r_rigid_bond_restr 1.63 r_angle_refined_deg 1.394 r_mcbond_it 1.226 r_chiral_restr 0.105 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 4080 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling