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Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.5A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.12M mixture of 1,6-hexanediol,1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1M Tris-Bicine pH 8.5, 30% glycerol, PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.791 α = 90 b = 114.477 β = 92.04 c = 130.594 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 113 CCD ADSC QUANTUM 315r 2013-02-12 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) 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 2.5 65.3 99.6 0.06 0.06 15.8 3.9 74022 73752 76
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 2.5 2.64 100 0.132 0.132 1.1 4 10759
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 4G6G 2.5 64.61 70011 3717 99.53 0.21962 0.21696 0.2191 0.26864 0.2693 RANDOM 75.979
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] 0.26 0.36 -0.21 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.124 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 16.636 r_long_range_B_other 15.639 r_long_range_B_refined 15.628 r_scangle_other 12.681 r_mcangle_it 12.552 r_mcangle_other 12.551 r_mcbond_other 9.427 r_mcbond_it 9.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.124 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 16.636 r_long_range_B_other 15.639 r_long_range_B_refined 15.628 r_scangle_other 12.681 r_mcangle_it 12.552 r_mcangle_other 12.551 r_mcbond_other 9.427 r_mcbond_it 9.426 r_scbond_it 9.01 r_scbond_other 9.01 r_dihedral_angle_1_deg 5.904 r_angle_refined_deg 1.144 r_angle_other_deg 0.808 r_chiral_restr 0.07 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.004 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 12005 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 212
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling