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Crystal structure of branching enzyme D501A mutant from Cyanothece sp. ATCC 51142
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 4.66 73.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.628 α = 90 b = 133.628 β = 90 c = 185.327 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 210 2014-11-22 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 1.95 50 100 0.042 59.4 12.9 122106
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 1.98 100 0.255 10.4 12
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 1.95 46.33 114265 6063 98.55 0.15777 0.15637 0.1693 0.18384 0.1926 RANDOM 24.553
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 35.794 r_dihedral_angle_4_deg 13.314 r_dihedral_angle_3_deg 13.116 r_long_range_B_refined 7.201 r_long_range_B_other 6.901 r_dihedral_angle_1_deg 6.709 r_scangle_other 5.456 r_scbond_it 3.839 r_scbond_other 3.836 r_mcangle_it 3.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.794 r_dihedral_angle_4_deg 13.314 r_dihedral_angle_3_deg 13.116 r_long_range_B_refined 7.201 r_long_range_B_other 6.901 r_dihedral_angle_1_deg 6.709 r_scangle_other 5.456 r_scbond_it 3.839 r_scbond_other 3.836 r_mcangle_it 3.025 r_mcangle_other 3.025 r_mcbond_it 2.43 r_mcbond_other 2.43 r_angle_refined_deg 2.059 r_angle_other_deg 0.957 r_chiral_restr 0.146 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 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 6270 Nucleic Acid Atoms Solvent Atoms 873 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing