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Crystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with toluenesulfonylmethylisocyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAG PDB ENTRY 3DAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 281 0.5 mM toluenesulfonylmethylisocyanide, 0.1 M Tris, 0.02 M MgCl2, 25%(v/v) pentaerythritol propoxylate 426, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.88 α = 90 b = 141.88 β = 90 c = 95.48 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2010-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 20 98.8 20.9 2.93 24511 24511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 98 8.1 2.9 2710
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 (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 THROUGHOUT PDB ENTRY 3DAG 2.5 20 23266 23266 1243 98.86 0.18703 0.18703 0.18394 0.1813 0.24495 0.2418 RANDOM 46.312
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] -0.1 -0.05 -0.1 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.303 r_angle_refined_deg 2.038 r_chiral_restr 0.136 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.303 r_angle_refined_deg 2.038 r_chiral_restr 0.136 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5276 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 110
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction