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Crystal Structure of Endonuclease IV (BA4508) from Bacillus anthracis at 2.57A Resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QTW PDB ENTRY 1QTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 5000, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.886 α = 90 b = 55.39 β = 89.43 c = 64.972 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 4 Rh coated Si mirror 2004-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87000 SRS PX9.6
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 2.57 50 93.7 0.061 14 2.7 10633 10633
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 2.57 2.66 86.6 0.242 4 2.5 964
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 (All) 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 1QTW 2.57 22.83 10606 10606 532 100 0.15478 0.15478 0.15117 0.1575 0.22808 0.2278 RANDOM 41.983
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] -0.25 -0.12 0.2 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.336 r_dihedral_angle_4_deg 21.146 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_1_deg 8.282 r_scangle_it 2.308 r_angle_refined_deg 1.649 r_scbond_it 1.468 r_angle_other_deg 0.939 r_mcangle_it 0.837 r_mcbond_it 0.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.336 r_dihedral_angle_4_deg 21.146 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_1_deg 8.282 r_scangle_it 2.308 r_angle_refined_deg 1.649 r_scbond_it 1.468 r_angle_other_deg 0.939 r_mcangle_it 0.837 r_mcbond_it 0.656 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.208 r_nbd_other 0.198 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.172 r_symmetry_vdw_refined 0.114 r_mcbond_other 0.113 r_chiral_restr 0.099 r_nbtor_other 0.092 r_metal_ion_refined 0.074 r_xyhbond_nbd_other 0.048 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing