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Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 in complex with maltohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 magnesium chloride, ethanol, HEPES-NaOH
Crystal Properties Matthews coefficient Solvent content 4.58 73.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.126 α = 90 b = 134.126 β = 90 c = 184.325 γ = 90
Symmetry Space Group P 41 21 2
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 270 2015-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 3 50 99.8 0.128 40.17 13.9 34353
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 3 3.05 100 0.322 15.12 14.4
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 5GQU 3 47.42 32532 1730 99.71 0.1658 0.16271 0.1681 0.22379 0.2246 RANDOM 39.693
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_3_deg 17.282 r_dihedral_angle_4_deg 15.438 r_long_range_B_refined 7.29 r_long_range_B_other 7.281 r_dihedral_angle_1_deg 6.855 r_scangle_other 5.67 r_mcangle_other 4.058 r_mcangle_it 4.057 r_scbond_it 3.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_3_deg 17.282 r_dihedral_angle_4_deg 15.438 r_long_range_B_refined 7.29 r_long_range_B_other 7.281 r_dihedral_angle_1_deg 6.855 r_scangle_other 5.67 r_mcangle_other 4.058 r_mcangle_it 4.057 r_scbond_it 3.681 r_scbond_other 3.68 r_mcbond_it 2.577 r_mcbond_other 2.574 r_angle_refined_deg 1.89 r_angle_other_deg 0.857 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6273 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling MOLREP phasing