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Three-dimensional structure of the photoproduct state of GAF3 from Slr1393 of Synechocystis sp. PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 0.1 M NaCl, 0.1 M CAPSO pH 9.5, 0.175 M LiSO4, 14% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.286 α = 90 b = 75.286 β = 90 c = 71.38 γ = 120
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 6M-F KB mirrors 2015-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976252 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.86 65.2 94.4 0.027 1 25.79 3.89 18191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.98 78.9 0.92 3.37 3.07
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 5M85 1.86 65.2 17263 921 94.33 0.19596 0.1941 0.1997 0.22872 0.2311 RANDOM 38.426
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] 0.53 0.26 0.53 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.767 r_dihedral_angle_4_deg 15.857 r_dihedral_angle_3_deg 12.798 r_long_range_B_other 8.055 r_long_range_B_refined 8.03 r_dihedral_angle_1_deg 6.737 r_scangle_other 6.544 r_scbond_it 4.414 r_scbond_other 4.411 r_mcangle_it 4.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.767 r_dihedral_angle_4_deg 15.857 r_dihedral_angle_3_deg 12.798 r_long_range_B_other 8.055 r_long_range_B_refined 8.03 r_dihedral_angle_1_deg 6.737 r_scangle_other 6.544 r_scbond_it 4.414 r_scbond_other 4.411 r_mcangle_it 4.394 r_mcangle_other 4.393 r_mcbond_it 3.492 r_mcbond_other 3.49 r_angle_refined_deg 2.376 r_angle_other_deg 1.48 r_chiral_restr 0.144 r_bond_refined_d 0.02 r_gen_planes_other 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.005 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 1304 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing