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Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.148 α = 90 b = 114.385 β = 92.32 c = 58.135 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 2016-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.93 58.09 99.5 0.087 0.075 0.998 9.8 4.3 45429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 94.6 0.751 0.669 0.662 1.4 3.9
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 1CC8 1.93 58.09 42701 2301 99.48 0.19782 0.19542 0.2024 0.24175 0.2431 RANDOM 31.254
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] -0.6 0.41 -1.21 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.443 r_dihedral_angle_4_deg 20.123 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_1_deg 5.997 r_long_range_B_refined 5.824 r_long_range_B_other 5.774 r_scangle_other 3.962 r_mcangle_other 2.94 r_mcangle_it 2.939 r_scbond_it 2.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.443 r_dihedral_angle_4_deg 20.123 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_1_deg 5.997 r_long_range_B_refined 5.824 r_long_range_B_other 5.774 r_scangle_other 3.962 r_mcangle_other 2.94 r_mcangle_it 2.939 r_scbond_it 2.411 r_scbond_other 2.411 r_mcbond_it 1.852 r_mcbond_other 1.851 r_angle_refined_deg 1.394 r_angle_other_deg 0.876 r_chiral_restr 0.081 r_bond_refined_d 0.01 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 4448 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing