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Three-dimensional structure of the intermediate state of GAF3 from Slr1393 of Synechocystis sp. PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 0.1 M NaCl, 0.1 M LiSO4, 0.1 M CAPSO pH 9.5, 12% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.101 α = 90 b = 75.101 β = 90 c = 71.21 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 2015-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.954 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 2.1 71.21 99.6 0.063 1 33.34 20.07 13390
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 2.1 2.23 98.2 0.959 5.96 19.2
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 5DFX 2.1 65.04 12751 640 99.76 0.17213 0.16971 0.22233 0.2233 RANDOM 43.486
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] -0.19 -0.09 -0.19 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_4_deg 14.973 r_dihedral_angle_3_deg 14.316 r_long_range_B_other 8.744 r_long_range_B_refined 8.715 r_scangle_other 7.307 r_dihedral_angle_1_deg 6.721 r_scbond_it 5.098 r_scbond_other 5.055 r_mcangle_it 4.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_4_deg 14.973 r_dihedral_angle_3_deg 14.316 r_long_range_B_other 8.744 r_long_range_B_refined 8.715 r_scangle_other 7.307 r_dihedral_angle_1_deg 6.721 r_scbond_it 5.098 r_scbond_other 5.055 r_mcangle_it 4.406 r_mcangle_other 4.403 r_mcbond_it 3.636 r_mcbond_other 3.6 r_angle_refined_deg 2.43 r_angle_other_deg 1.294 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_other 0.018 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 1315 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing