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Crystal structure of AmyK38 with rubidium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model of native AmyK38 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Soaking of native crystals 6.8 293 PEG 8000, rubidium acetate, glycerol, MES-NaOH, Tris-HCl, pH 6.8, Soaking of native crystals, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.52 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.605 α = 90 b = 132.605 β = 90 c = 132.605 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.8100 SPring-8 BL44B2
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 2.7 100 99.7 0.093 27.4 12.7 21600 21600 39.8
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 2.7 2.8 100 0.262 10.9 2109
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Model of native AmyK38 structure 2.7 59.3 21600 21495 1079 99.2 0.213 0.269 RANDOM 29.3
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 5.88 c_scbond_it 4.62 c_mcangle_it 4.51 c_mcbond_it 3.16 c_angle_deg 1.3 c_improper_angle_d 0.76 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 5.88 c_scbond_it 4.62 c_mcangle_it 4.51 c_mcbond_it 3.16 c_angle_deg 1.3 c_improper_angle_d 0.76 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3908 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing