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Crystal structure of branching enzyme Y500A 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 4.47 72.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.928 α = 90 b = 133.928 β = 90 c = 184.734 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 1.85 50 100 0.036 68.4 14.3 142937
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 1.85 1.88 100 0.251 11.8 14.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5GQU 1.85 47.35 134668 7119 99.26 0.15863 0.15754 0.17915 0.183 RANDOM 25.24
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 35.923 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_3_deg 13.154 r_long_range_B_refined 7.463 r_long_range_B_other 7.2 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.899 r_scbond_it 4.151 r_scbond_other 4.15 r_mcangle_other 3.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_3_deg 13.154 r_long_range_B_refined 7.463 r_long_range_B_other 7.2 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.899 r_scbond_it 4.151 r_scbond_other 4.15 r_mcangle_other 3.367 r_mcangle_it 3.364 r_mcbond_it 2.713 r_mcbond_other 2.706 r_angle_refined_deg 2.336 r_angle_other_deg 1.03 r_chiral_restr 0.16 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 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 6266 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing