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The Structure of the Ycf54 protein from Synechocystis sp. PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.2M ammonium fluoride, 2.4M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.34 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.73 α = 90 b = 45.93 β = 90 c = 119.28 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 2012-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9686 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.33 59.65 99.5 16.5 4.5 27322
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 3HZE 1.33 59.65 25912 1368 99.41 0.15034 0.14925 0.149 0.17147 0.1722 RANDOM 14.916
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] -0.23 0.35 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.574 r_sphericity_free 28.206 r_dihedral_angle_4_deg 22.19 r_sphericity_bonded 12.521 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.365 r_rigid_bond_restr 3.936 r_angle_refined_deg 1.402 r_angle_other_deg 0.783 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.574 r_sphericity_free 28.206 r_dihedral_angle_4_deg 22.19 r_sphericity_bonded 12.521 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.365 r_rigid_bond_restr 3.936 r_angle_refined_deg 1.402 r_angle_other_deg 0.783 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 863 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling PHASER phasing