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The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F46 PDB ENTRY 3F46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 50% MPD, 100mM Tris-HCl, 100mM Ammonium dihydrogen phosphate, 1mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.63 α = 90 b = 97.63 β = 90 c = 165.75 γ = 90
Symmetry Space Group I 41 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 100 CCD MARMOSAIC 225 mm CCD Dynamically bendable mirror 2008-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9919 SLS X10SA
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 2.15 48.81 95.1 0.041 17.4 3.6 21096 -3 52.333
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 2.15 2.3 85.8 0.424 3.6 3.5 12007
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3F46 2.15 48.81 21095 1084 95.09 0.171 0.17 0.1726 0.203 0.2102 RANDOM 48.549
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] 0.64 0.64 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.084 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 5.504 r_scangle_it 3.605 r_scbond_it 2.298 r_angle_refined_deg 1.74 r_mcangle_it 1.243 r_mcbond_it 0.825 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.084 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 5.504 r_scangle_it 3.605 r_scbond_it 2.298 r_angle_refined_deg 1.74 r_mcangle_it 1.243 r_mcbond_it 0.825 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 103
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction REFMAC phasing