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Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.
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 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.67 α = 90 b = 128.456 β = 90 c = 86.711 γ = 90
Symmetry Space Group C 2 2 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 1.85 50 99.9 0.086 7.1 5.4 49022
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 1.85 1.88 100 0.786 1.8 5
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 4G9K 1.85 29.48 49008 2632 92.52 0.18341 0.18227 0.1903 0.2043 0.2097 RANDOM 24.261
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 -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.089 r_dihedral_angle_4_deg 15.5 r_dihedral_angle_3_deg 13.426 r_long_range_B_refined 5.671 r_dihedral_angle_1_deg 5.626 r_long_range_B_other 5.389 r_scangle_other 1.789 r_mcangle_it 1.626 r_mcangle_other 1.626 r_angle_refined_deg 1.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.089 r_dihedral_angle_4_deg 15.5 r_dihedral_angle_3_deg 13.426 r_long_range_B_refined 5.671 r_dihedral_angle_1_deg 5.626 r_long_range_B_other 5.389 r_scangle_other 1.789 r_mcangle_it 1.626 r_mcangle_other 1.626 r_angle_refined_deg 1.443 r_angle_other_deg 1.121 r_scbond_it 1.043 r_scbond_other 1.043 r_mcbond_it 0.914 r_mcbond_other 0.914 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3578 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 317
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing