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Crystal structure of yeast GGA1_GAE domain-C2221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 289 20% PEG 5000 MME, 0.2 M (NH4)2SO4, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.04 α = 90 b = 110.94 β = 90 c = 90.88 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 CCD ADSC QUANTUM 315r 2014-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 2.25 50 99.8 7.3 7.3 13301
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 5CN1 2.25 48.63 12630 653 99.65 0.23317 0.23128 0.2342 0.27016 0.2751 RANDOM 43.614
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] 0.62 -0.54 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 18.945 r_dihedral_angle_4_deg 11.292 r_long_range_B_refined 7.07 r_dihedral_angle_1_deg 7.064 r_long_range_B_other 7.06 r_scangle_other 4.814 r_mcangle_it 4.255 r_mcangle_other 4.253 r_scbond_it 3.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 18.945 r_dihedral_angle_4_deg 11.292 r_long_range_B_refined 7.07 r_dihedral_angle_1_deg 7.064 r_long_range_B_other 7.06 r_scangle_other 4.814 r_mcangle_it 4.255 r_mcangle_other 4.253 r_scbond_it 3.142 r_scbond_other 3.14 r_mcbond_it 2.801 r_mcbond_other 2.796 r_angle_refined_deg 1.546 r_angle_other_deg 0.756 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1744 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction PHASER phasing Coot model building