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Crystal structure of Bacillus subtilis dimanganese(II) NrdF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 PEG 4000, lithium sulfate, pH 6.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.525 α = 90 b = 112.912 β = 90 c = 51.286 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD 2011-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 1.9 50 49535
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 1.9 31.29 49350 2471 96.18 0.1876 0.1857 0.1897 0.224 0.2298 RANDOM 29.851
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] -1.76 -1.75 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.007 r_dihedral_angle_3_deg 13.865 r_dihedral_angle_4_deg 13.234 r_dihedral_angle_1_deg 4.699 r_scangle_it 3.04 r_scbond_it 1.823 r_angle_refined_deg 1.089 r_mcangle_it 1.067 r_mcbond_it 0.537 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.007 r_dihedral_angle_3_deg 13.865 r_dihedral_angle_4_deg 13.234 r_dihedral_angle_1_deg 4.699 r_scangle_it 3.04 r_scbond_it 1.823 r_angle_refined_deg 1.089 r_mcangle_it 1.067 r_mcbond_it 0.537 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction