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Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 50mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2%(v/v) ethylene glycol, 5%(v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.11 60.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.854 α = 90 b = 115.795 β = 90 c = 166.499 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300HE 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.4 50 97.3 0.095 7.9 4.9 18371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.46 98.6 0.773 1.3 4.7
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 4G9K 3.4 20 15012 807 82.13 0.2118 0.20709 0.29865 0.3006 RANDOM 62.912
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] 7.37 -3.17 -4.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.546 r_dihedral_angle_3_deg 20.583 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_1_deg 8.191 r_angle_refined_deg 1.609 r_angle_other_deg 0.838 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.546 r_dihedral_angle_3_deg 20.583 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_1_deg 8.191 r_angle_refined_deg 1.609 r_angle_other_deg 0.838 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing