☰ Navigation Tabs
Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibrio marinus in a ferricyanide-oxidized condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M PIPES, 15% PEG 3350, 300MM LITHIUM SULFATE, 5MM DTT, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.628 α = 90 b = 116.943 β = 91.42 c = 113.337 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 90 CCD RAYONIX MX-225 2010-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 1.32 20 99.2 12.6 3.8 459508
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 1.32 1.34 97.3 0.496 3.2 3.2
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 3AYX 1.32 19.89 425556 22442 97.34 0.13199 0.13063 0.1304 0.15804 0.1576 RANDOM 19.001
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] 2.66 0.84 -0.74 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_sphericity_free 32.164 r_dihedral_angle_4_deg 15.503 r_sphericity_bonded 15.012 r_dihedral_angle_3_deg 11.9 r_dihedral_angle_1_deg 5.934 r_rigid_bond_restr 2.509 r_angle_refined_deg 1.347 r_chiral_restr 0.09 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_sphericity_free 32.164 r_dihedral_angle_4_deg 15.503 r_sphericity_bonded 15.012 r_dihedral_angle_3_deg 11.9 r_dihedral_angle_1_deg 5.934 r_rigid_bond_restr 2.509 r_angle_refined_deg 1.347 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13529 Nucleic Acid Atoms Solvent Atoms 2189 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing