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Structure of a covalent intermediate in Thermus thermophilus amylomaltase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.4-0.8 M sodium malonate pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.405 α = 90 b = 92.405 β = 90 c = 154.115 γ = 120
Symmetry Space Group P 31 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 4 2003-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.9 30 100 0.084 24 46013 57412
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 1.9 1.97 100 0.794 2.4
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 1CWY 2.05 29.62 46013 2425 100 0.18763 0.18613 0.1871 0.21593 0.2177 RANDOM 27.623
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] 0.4 0.2 0.4 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.197 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 15.372 r_dihedral_angle_1_deg 5.326 r_scangle_it 2.281 r_scbond_it 1.457 r_angle_refined_deg 1.284 r_mcangle_it 1.108 r_mcbond_it 0.614 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.197 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 15.372 r_dihedral_angle_1_deg 5.326 r_scangle_it 2.281 r_scbond_it 1.457 r_angle_refined_deg 1.284 r_mcangle_it 1.108 r_mcbond_it 0.614 r_nbtor_refined 0.314 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.065 r_gen_planes_refined 0.026 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4061 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing