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Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Ammonium sulphate, K/Na tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.75 α = 90 b = 86.75 β = 90 c = 179.08 γ = 120
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 mirrors 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.7 43.36 98.7 0.04 25.2 7.3 28380 28380 27.43
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) 1.7 1.79 95.6 0.38 4.8 5.7 3948
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 1OYR 1.702 34.65 26895 26895 1413 98.42 0.21384 0.21227 0.2718 0.24414 0.2927 RANDOM 20.643
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] -0.27 -0.14 -0.27 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.699 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 14.523 r_dihedral_angle_1_deg 8.631 r_scangle_it 3.499 r_scbond_it 2.235 r_angle_refined_deg 1.462 r_mcangle_it 1.246 r_mcbond_it 0.76 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.699 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 14.523 r_dihedral_angle_1_deg 8.631 r_scangle_it 3.499 r_scbond_it 2.235 r_angle_refined_deg 1.462 r_mcangle_it 1.246 r_mcbond_it 0.76 r_chiral_restr 0.099 r_bond_refined_d 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 25
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling