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High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KL8 PDB entry 4KL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.23 α = 90 b = 108.91 β = 90 c = 136.34 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 ADSC QUANTUM 315r 2011-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9500 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 30 90.5 0.062 10.7 3.6 228384 206663 21.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 61.1 0.628 1.03 2.4 35250
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4KL8 1.55 25 228354 196199 10443 90.49 0.14914 0.14729 0.1481 0.18389 0.1844 RANDOM 18.213
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] -0.09 -0.54 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.176 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 11.409 r_scangle_it 6.047 r_dihedral_angle_1_deg 5.539 r_scbond_it 4.265 r_mcangle_it 3.019 r_rigid_bond_restr 2.217 r_mcbond_it 2.019 r_angle_refined_deg 1.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.176 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 11.409 r_scangle_it 6.047 r_dihedral_angle_1_deg 5.539 r_scbond_it 4.265 r_mcangle_it 3.019 r_rigid_bond_restr 2.217 r_mcbond_it 2.019 r_angle_refined_deg 1.263 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11916 Nucleic Acid Atoms Solvent Atoms 1770 Heterogen Atoms 97
Software Software Software Name Purpose Xnemo data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling