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The Structure of apo-MntR from Bacillus subtilis, Native Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HYF PDB ENTRY 2HYF, chain D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 15% PEG 4000, 0.2 M ammonium sulfate, 5 mM cobalt(II) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42 α = 90 b = 42 β = 90 c = 149.1 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
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 2.8 74.5 99.9 0.041 8.8 13.2 4162 2 104
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 2.8 2.95 99.9 0.35 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 PDB ENTRY 2HYF, chain D 2.8 20 3695 423 99.9 0.28016 0.27353 0.2611 0.34206 0.3333 RANDOM 97.859
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] 2.39 1.19 2.39 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.937 r_dihedral_angle_4_deg 22.947 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_1_deg 5.023 r_scangle_it 1.414 r_angle_refined_deg 1.092 r_scbond_it 0.835 r_mcangle_it 0.579 r_mcbond_it 0.328 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.937 r_dihedral_angle_4_deg 22.947 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_1_deg 5.023 r_scangle_it 1.414 r_angle_refined_deg 1.092 r_scbond_it 0.835 r_mcangle_it 0.579 r_mcbond_it 0.328 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1102 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling EPMR phasing