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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 3AZY PDB ENTRY 3AZY
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 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.305 α = 90 b = 120.305 β = 90 c = 107.154 γ = 90
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 Focusing Mirror 2010-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
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 1.87 30 99.7 0.065 27.4 6.2 125924 125562 1 39
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 1.87 1.94 100 0.517 3.9 6.1 12561
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 3AZY 1.87 27.5 125430 6298 99.63 0.15348 0.1517 0.1693 0.18771 0.2023 RANDOM 28.415
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] 0.18 0.18 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.729 r_dihedral_angle_4_deg 13.339 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_1_deg 6.994 r_scangle_it 5.128 r_scbond_it 3.378 r_mcangle_it 2.289 r_rigid_bond_restr 1.768 r_angle_refined_deg 1.406 r_mcbond_it 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.729 r_dihedral_angle_4_deg 13.339 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_1_deg 6.994 r_scangle_it 5.128 r_scbond_it 3.378 r_mcangle_it 2.289 r_rigid_bond_restr 1.768 r_angle_refined_deg 1.406 r_mcbond_it 1.348 r_chiral_restr 0.101 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 8123 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling