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Structure of the T18D small subunit mutant of D. fructosovorans NiFe- hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQW PDB ENTRY 1YQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 VAPOR DIFFUSION, PH 6.3, 293K; PEG6000, MES, UNDER AIR
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.8 α = 90 b = 99.9 β = 91.9 c = 183.3 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 2009-07-02 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 2.6 40 99.2 0.07 13 3.8 70368
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 2.6 2.76 97.8 0.36 3.4 3.8
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 1YQW 2.6 25 66841 3462 99.04 0.1999 0.19777 0.1991 0.24133 0.2427 RANDOM 49.085
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] 3.81 2.12 0.18 -4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_1_deg 6.311 r_angle_refined_deg 1.599 r_mcangle_it 1.059 r_scbond_it 0.815 r_mcbond_it 0.685 r_chiral_restr 0.101 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_1_deg 6.311 r_angle_refined_deg 1.599 r_mcangle_it 1.059 r_scbond_it 0.815 r_mcbond_it 0.685 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 18408 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing