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Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ODC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 1% (w/v) polyethylene glycol 3350, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD, 10 mM CoM-SH and 1 ul of precipitant. The crystals appear after 1-2 weeks and are cryoprotected in the crystallization solution supplemented with 30% glycerol
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 370.528 α = 90 b = 97.077 β = 109.43 c = 135.149 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97916 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.4 48.54 100 0.189 0.071 0.992 7.2 8 176807 30.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.507 0.188 0.332 3.6 8.2
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 5ODC 2.4 48.54 176789 8805 99.94 0.2035 0.2015 0.2298 0.2408 0.2729 RANDOM 64.65
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] 4.2309 3.2754 -1.1058 -3.1251
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.84 t_omega_torsion 1.29 t_angle_deg 1.05 t_bond_d 0.006 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.84 t_omega_torsion 1.29 t_angle_deg 1.05 t_bond_d 0.006 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 61987 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 1111
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing