☰ Navigation Tabs
Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains in complex with branched pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MES buffer, PEG 20000, PEG 4000, PEG 3350, sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.508 α = 90 b = 61.051 β = 106.11 c = 99.808 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 100 PIXEL DECTRIS PILATUS 2M-F 2021-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.55 47.9 98.8 0.049 0.032 13.1 3.3 106919
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.6 0.4 0.258 2.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 47.94 101632 5267 98.77 0.17433 0.17361 0.1581 0.1886 0.1758 RANDOM 18.582
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.824 r_dihedral_angle_4_deg 18.086 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 4.639 r_long_range_B_other 4.415 r_scangle_other 3.127 r_angle_other_deg 2.605 r_scbond_it 2.05 r_scbond_other 2.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.824 r_dihedral_angle_4_deg 18.086 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 4.639 r_long_range_B_other 4.415 r_scangle_other 3.127 r_angle_other_deg 2.605 r_scbond_it 2.05 r_scbond_other 2.049 r_mcangle_it 1.756 r_mcangle_other 1.756 r_angle_refined_deg 1.553 r_mcbond_it 1.169 r_mcbond_other 1.166 r_chiral_restr 0.081 r_bond_other_d 0.034 r_gen_planes_other 0.014 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5077 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing