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Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.111 α = 90 b = 101.833 β = 90 c = 145.508 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 77 IMAGE PLATE MARRESEARCH mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.65 30 0.086 6.2 111530
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 1.65 1.71 0.361 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.65 30 100105 5258 95.96 0.15499 0.15369 0.1534 0.17951 0.1797 RANDOM 19.813
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] 1.84 -0.09 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 19.461 r_dihedral_angle_3_deg 12.199 r_dihedral_angle_1_deg 6.875 r_scangle_it 2.948 r_scbond_it 1.921 r_angle_refined_deg 1.341 r_mcangle_it 1.104 r_mcbond_it 0.711 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 19.461 r_dihedral_angle_3_deg 12.199 r_dihedral_angle_1_deg 6.875 r_scangle_it 2.948 r_scbond_it 1.921 r_angle_refined_deg 1.341 r_mcangle_it 1.104 r_mcbond_it 0.711 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.093 r_metal_ion_refined 0.025 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7687 Nucleic Acid Atoms Solvent Atoms 1021 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing