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Structure of methylene blue-treated anaerobically purified D. fructosovorans NiFe-hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FRV PDB ENTRY 2FRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 CRYSTAL GROWN IN GLOVE BOX, PEG6000, MES, PH 6.2, SOAKED 2 HOURS IN A METHYLENE BLUE SOLUTION BEFORE FLASH-FREEZING AND DATA COLLECTION
Crystal Properties Matthews coefficient Solvent content 2.2 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.28 α = 90 b = 99.55 β = 91.16 c = 184.02 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 100 CCD ADSC CCD 2000-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.3 23.9 94.9 0.06 14.4 3.3 99290
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 2.3 2.44 76.5 0.21 3.3 1.7
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 PDB ENTRY 2FRV 2.3 23.9 94319 4970 94.88 0.15219 0.15066 0.1546 0.18141 0.1853 RANDOM 32.856
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] 2.59 1.41 -0.79 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_3_deg 14.323 r_dihedral_angle_1_deg 4.866 r_scbond_it 1.668 r_mcangle_it 1.609 r_angle_refined_deg 1.358 r_mcbond_it 1.024 r_chiral_restr 0.084 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_3_deg 14.323 r_dihedral_angle_1_deg 4.866 r_scbond_it 1.668 r_mcangle_it 1.609 r_angle_refined_deg 1.358 r_mcbond_it 1.024 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18403 Nucleic Acid Atoms Solvent Atoms 1048 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing