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Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 35% (v/v) PEG 400, 0.1M Tris-HCl pH 8.5, 0.15M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.576 α = 90 b = 98.576 β = 90 c = 88.267 γ = 90
Symmetry Space Group P 43 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 90 CCD ADSC QUANTUM 315 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.1 20 99.9 0.052 11.7 4.2 25983 25983 38.3
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 2.1 2.21 100 0.442 3.2 4.2 4806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 20 24627 1319 99.85 0.2157 0.21366 0.2406 0.25435 0.2757 RANDOM 19.958
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] -0.1 -0.1 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.303 r_dihedral_angle_4_deg 18.859 r_dihedral_angle_3_deg 17.859 r_dihedral_angle_1_deg 6.453 r_scangle_it 2.114 r_scbond_it 1.323 r_angle_refined_deg 1.196 r_mcangle_it 0.853 r_mcbond_it 0.46 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.303 r_dihedral_angle_4_deg 18.859 r_dihedral_angle_3_deg 17.859 r_dihedral_angle_1_deg 6.453 r_scangle_it 2.114 r_scbond_it 1.323 r_angle_refined_deg 1.196 r_mcangle_it 0.853 r_mcbond_it 0.46 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2890 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 53
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling