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Klebsiella pneumoniae maltohexaose-producing alpha-amylase in complex with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9US3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.2 293 8% polyethylene glycol 3000,
4% polyethylene glycol 3350,
40 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.913 α = 90 b = 108.244 β = 96.765 c = 82.284 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2013-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
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 1.95 100 100 0.156 12 14.4 94976
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 1.95 1.98 0.795 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 9US3 1.95 29.681 92514 4624 97.527 0.191 0.1891 0.1963 0.2266 0.2319 26.503
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] 0.005 -0.008 0.013 -0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 12.629 r_dihedral_angle_1_deg 6.665 r_lrange_it 3.555 r_lrange_other 3.516 r_mcangle_it 1.22 r_mcangle_other 1.22 r_angle_refined_deg 1.178 r_angle_other_deg 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 12.629 r_dihedral_angle_1_deg 6.665 r_lrange_it 3.555 r_lrange_other 3.516 r_mcangle_it 1.22 r_mcangle_other 1.22 r_angle_refined_deg 1.178 r_angle_other_deg 1.11 r_scangle_it 1.017 r_scangle_other 1.017 r_mcbond_it 0.67 r_mcbond_other 0.67 r_scbond_it 0.572 r_scbond_other 0.572 r_nbd_refined 0.175 r_symmetry_nbd_other 0.164 r_nbd_other 0.161 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbd_refined 0.094 r_metal_ion_refined 0.087 r_symmetry_nbtor_other 0.071 r_chiral_restr_other 0.045 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10353 Nucleic Acid Atoms Solvent Atoms 1081 Heterogen Atoms 301
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing