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Crystal Structure of ETDA-treated BdbD (Reduced)
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 VAPOR DIFFUSION, SITTING DROP 6.5 289 25-27% PEG2000, 100mM Ammonium Acetate, 100mM MES, pH6.5, 0.1mM EDTA, 0.1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.9 35.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.55 α = 90 b = 43.63 β = 107.4 c = 54.58 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 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9798 Diamond I02
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 1.4 25.08 97.8 0.058 9.6 3.4 33423 33423 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) 1.4 1.48 99.6 0.351 2.4 3.5
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 1.4 22.67 33423 31745 1662 97.61 0.21114 0.20881 0.2033 0.25439 0.2486 RANDOM 20.982
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] -0.38 -0.14 1.28 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_dihedral_angle_4_deg 14.089 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 4.841 r_sphericity_bonded 4.159 r_sphericity_free 4.13 r_scangle_it 3.429 r_scbond_it 2.214 r_mcangle_it 1.604 r_rigid_bond_restr 1.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_dihedral_angle_4_deg 14.089 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 4.841 r_sphericity_bonded 4.159 r_sphericity_free 4.13 r_scangle_it 3.429 r_scbond_it 2.214 r_mcangle_it 1.604 r_rigid_bond_restr 1.252 r_angle_refined_deg 1.207 r_mcbond_it 0.988 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1611 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 5
Software Software Software Name Purpose ADSC data collection BP3 model building REFMAC refinement MOSFLM data reduction SCALA data scaling BP3 phasing