☰ Navigation Tabs
The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 49% MPD, 100mM Tris-HCl, 50mM Ammonium dihydrogen phosphate, 1mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.35 α = 90 b = 96.35 β = 90 c = 166.61 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 2008-03-08 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 1.95 41.7 96.9 0.064 17.2 7.9 28094 -3 40.584
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 1.95 2 95.8 0.701 4.2 7.7 15394
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 3DAG 1.95 40 28091 1430 97.03 0.167 0.165 0.1675 0.205 0.2059 RANDOM 37.913
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] 0.87 0.87 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.999 r_dihedral_angle_4_deg 21.103 r_dihedral_angle_3_deg 14.794 r_dihedral_angle_1_deg 5.209 r_scangle_it 3.842 r_scbond_it 2.43 r_angle_refined_deg 1.599 r_mcangle_it 1.326 r_mcbond_it 0.97 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.999 r_dihedral_angle_4_deg 21.103 r_dihedral_angle_3_deg 14.794 r_dihedral_angle_1_deg 5.209 r_scangle_it 3.842 r_scbond_it 2.43 r_angle_refined_deg 1.599 r_mcangle_it 1.326 r_mcbond_it 0.97 r_nbtor_refined 0.304 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 49
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction REFMAC phasing