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Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 283 30%(v/v) 2-methyl-2,4-pentane-d12-diol, 10 mM glucose-d12, 25 mM Tris-d11-DCl in D2O
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.705 α = 90 b = 98.485 β = 90 c = 126.86 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX225HE 2015-04-10 M SINGLE WAVELENGTH 2 1 neutron 100 DIFFRACTOMETER iBIX 2015-03-21 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.8000 SPring-8 BL26B1 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 1.8-5.8 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.04 50 99.9 0.059 0.062 1 19.7 8.5 397623 2 2.2 20 90.1 0.22 0.266 0.92 4.9 2.6 38335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.07 0.461 0.496 0.924 4.1 7.2 2 2.2 2.32 0.394 0.473 0.57 2.3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.04 41.69 1.34 397425 19868 99.78 0.143 0.1428 0.1426 0.1474 0.1472 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.2 17.94 38312 1893 88.91 0.1909 0.1893 0.2202
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.819 f_dihedral_angle_d 18.819 f_angle_d 1.213 f_angle_d 1.213 f_chiral_restr 0.095 f_chiral_restr 0.095 f_bond_d 0.014 f_bond_d 0.014 f_plane_restr 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6188 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement STARGazer data reduction SCALA data scaling PHASER phasing