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Crystal structure of yeast GGA1_GAE domain-P21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 289 1.2 M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.007 α = 90 b = 53.585 β = 103.57 c = 71.547 γ = 90
Symmetry Space Group P 1 21 1
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 2013-10-26 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 2.3 50 99.6 15.3 4.3 21922
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 3MNM 2.31 42.48 20721 1119 99.03 0.21519 0.21235 0.216 0.26972 0.2717 RANDOM 40.371
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] -1.15 -0.87 1.27 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.756 r_dihedral_angle_3_deg 20.455 r_dihedral_angle_4_deg 17.009 r_dihedral_angle_1_deg 6.964 r_long_range_B_refined 6.688 r_long_range_B_other 6.682 r_scangle_other 4.662 r_mcangle_it 4.24 r_mcangle_other 4.239 r_scbond_it 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.756 r_dihedral_angle_3_deg 20.455 r_dihedral_angle_4_deg 17.009 r_dihedral_angle_1_deg 6.964 r_long_range_B_refined 6.688 r_long_range_B_other 6.682 r_scangle_other 4.662 r_mcangle_it 4.24 r_mcangle_other 4.239 r_scbond_it 3.001 r_scbond_other 2.999 r_mcbond_it 2.71 r_mcbond_other 2.71 r_angle_refined_deg 1.627 r_angle_other_deg 0.812 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 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 3393 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing Coot model building