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The Structure of the Ycf54 A9G mutant protein from Synechocystis sp. PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.1M trisodium citrate, 2.4M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.2 α = 90 b = 46.13 β = 90 c = 119.66 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 6M 2013-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.5 24.54 99 0.08 0.04 10.9 6.1 18771 17.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 98.2 0.77 0.35 2.3 6.4 8496
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 5M2P 1.5 24.54 17771 960 98.76 0.18503 0.18204 0.1901 0.24331 0.2471 RANDOM 23.938
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] -1.37 -0.05 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.557 r_sphericity_free 26.59 r_dihedral_angle_4_deg 16.153 r_sphericity_bonded 12.696 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_1_deg 5.867 r_rigid_bond_restr 3.29 r_angle_refined_deg 1.384 r_angle_other_deg 0.779 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.557 r_sphericity_free 26.59 r_dihedral_angle_4_deg 16.153 r_sphericity_bonded 12.696 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_1_deg 5.867 r_rigid_bond_restr 3.29 r_angle_refined_deg 1.384 r_angle_other_deg 0.779 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 862 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling PHASER phasing