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Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2M ammonium sulfate, 20mM TrisCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.688 α = 90 b = 49.45 β = 90 c = 64.619 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MAC Science DIP-2030 1999-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.8 4583 4574 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.8
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 2DJH 2.3 39.27 4340 4307 207 99.25 0.23888 0.23801 0.2386 0.2573 0.2567 RANDOM 21.526
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] -1.02 -0.08 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_4_deg 21.948 r_dihedral_angle_3_deg 12.983 r_scangle_it 3.534 r_mcangle_it 2.64 r_scbond_it 2.301 r_angle_refined_deg 1.833 r_mcbond_it 1.509 r_dihedral_angle_1_deg 1.365 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_4_deg 21.948 r_dihedral_angle_3_deg 12.983 r_scangle_it 3.534 r_mcangle_it 2.64 r_scbond_it 2.301 r_angle_refined_deg 1.833 r_mcbond_it 1.509 r_dihedral_angle_1_deg 1.365 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 730 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 42
Software Software Software Name Purpose DIP-2030 data collection AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling