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Crystal Structure of BdbD from Bacillus subtilis (oxidised)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EU3 PDB ENTRY 3EU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, cryo-protected with 20% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.85 33.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.863 α = 90 b = 43.113 β = 107.5 c = 54.718 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 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 52.2 94.8 0.046 15.7 2.3 7198 7198 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 81.2 0.119 7.3 2.2
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 (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 3EU3 2.3 52.2 6805 6805 385 94.43 0.19601 0.1931 0.1944 0.24821 0.2447 RANDOM 19.203
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] -0.32 0.07 2.26 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_1_deg 9.752 r_scangle_it 2.068 r_scbond_it 1.297 r_angle_refined_deg 1.262 r_mcangle_it 0.783 r_mcbond_it 0.616 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_1_deg 9.752 r_scangle_it 2.068 r_scbond_it 1.297 r_angle_refined_deg 1.262 r_mcangle_it 0.783 r_mcbond_it 0.616 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.085 r_metal_ion_refined 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling