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Crystal structure of branching enzyme W610N mutant from Cyanothece sp. ATCC 51142 in complex with maltoheptaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GQW
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 4.47 72.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.025 α = 90 b = 134.025 β = 90 c = 185.06 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 2015-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 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 2.3 50 100 0.075 52.5 14.5 75270
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 2.3 2.34 100 0.261 15.1 14.6
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 5GQW 2.3 47.38 71338 3785 99.89 0.15076 0.14896 0.1607 0.18422 0.1906 RANDOM 25.994
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 r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_3_deg 14.381 r_long_range_B_refined 7.176 r_long_range_B_other 7.082 r_dihedral_angle_1_deg 6.798 r_scangle_other 5.775 r_scbond_it 3.877 r_scbond_other 3.875 r_mcangle_it 3.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_3_deg 14.381 r_long_range_B_refined 7.176 r_long_range_B_other 7.082 r_dihedral_angle_1_deg 6.798 r_scangle_other 5.775 r_scbond_it 3.877 r_scbond_other 3.875 r_mcangle_it 3.101 r_mcangle_other 3.101 r_mcbond_it 2.204 r_mcbond_other 2.203 r_angle_refined_deg 2.194 r_angle_other_deg 0.917 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 6267 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 448
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing