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Crystal Structure of phage 44RR small terminase gp16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TXQ PDB ENTRY 3TXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 12.5% PEG3350, 0.1M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.605 α = 90 b = 140.605 β = 90 c = 53.639 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 MARMOSAIC 300 mm CCD mirrors 2010-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.81 70.36 99.6 0.055 0.055 25 5.8 35876 35747 29.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 99.9 0.392 0.392 5 5.5 3570
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 3TXQ 1.81 70.36 34208 34075 1792 99.61 0.18866 0.18866 0.18699 0.1899 0.2199 0.2184 RANDOM 32.582
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] -1.16 -0.58 -1.16 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.84 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 4.569 r_scangle_it 2.687 r_scbond_it 1.662 r_angle_refined_deg 1.019 r_mcangle_it 1.003 r_mcbond_it 0.72 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.84 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 4.569 r_scangle_it 2.687 r_scbond_it 1.662 r_angle_refined_deg 1.019 r_mcangle_it 1.003 r_mcbond_it 0.72 r_nbtor_refined 0.296 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2887 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling