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Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XSJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.55 M lithium sulphate
0.1 M Bis-Tris propane (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.463 α = 90 b = 55.463 β = 90 c = 68.929 γ = 120
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 270 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
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 1.37 100 99.4 14.3 5 23888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.39 99.6 1.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XSJ 1.5 48.03 17594 947 96.3 0.14152 0.13959 0.17626 0.1853 RANDOM 20.218
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.252 r_dihedral_angle_2_deg 24.472 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 10.794 r_sphericity_bonded 10.532 r_dihedral_angle_1_deg 5.951 r_long_range_B_refined 4.775 r_long_range_B_other 4.299 r_scangle_other 3 r_scbond_other 2.467
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.252 r_dihedral_angle_2_deg 24.472 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 10.794 r_sphericity_bonded 10.532 r_dihedral_angle_1_deg 5.951 r_long_range_B_refined 4.775 r_long_range_B_other 4.299 r_scangle_other 3 r_scbond_other 2.467 r_scbond_it 2.448 r_mcangle_other 2.318 r_mcangle_it 2.315 r_mcbond_it 1.672 r_mcbond_other 1.66 r_angle_refined_deg 1.636 r_rigid_bond_restr 1.322 r_angle_other_deg 0.949 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 863 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing Coot model building