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Crystal structure of mitoNEET
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QD0 PDB entry 2QD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Crystals were grown by mixing 1 microliter of mitoNEET 23.3 mg/mL in 50 mM Tris HCl, 0.3 M NaCl, pH 8.5 with 1 microliter of 0.1 M Tris HCl, 1.5 ~ 1.8 M ammonium sulfate, pH 8.5 solution against the same solution. Crystals were appeared in 3 days and flash frozen by transfering into 0.1 M Tris HCl, 1.5 ~ 1.8 M amomnium acete, pH 8.5, 20% xylitol for a few minutes, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.9 68.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.64 α = 90 b = 58.64 β = 90 c = 177.61 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 225 mm CCD 2010-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.76 55.684 99.8 0.078 13.7 6.9 15831 15831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 100 0.514 0.514 1.5 6.6 2257
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2QD0 1.76 29.32 15856 15766 789 99.23 0.2032 0.2032 0.2019 0.2052 0.2285 0.2351 RANDOM 28.5501
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.897 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_1_deg 7.26 r_scangle_it 6.228 r_scbond_it 3.97 r_mcangle_it 2.791 r_angle_refined_deg 2.57 r_mcbond_it 1.849 r_angle_other_deg 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.897 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_1_deg 7.26 r_scangle_it 6.228 r_scbond_it 3.97 r_mcangle_it 2.791 r_angle_refined_deg 2.57 r_mcbond_it 1.849 r_angle_other_deg 1.146 r_mcbond_other 0.583 r_chiral_restr 0.168 r_bond_refined_d 0.034 r_gen_planes_refined 0.016 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 610 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 4
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection