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Single-stranded DNA-binding protein from bacteriophage Enc34 in complex with ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ODK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES, 30% Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.489 α = 90 b = 43.489 β = 90 c = 179.106 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 PIXEL DECTRIS PILATUS 6M 2016-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.56 59.6 99.7 0.071 0.036 0.999 9.5 4.8 27151
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.56 99.7 0.679 0.344 0.389 2.1 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5ODK 1.56 37.66 25751 1316 99.71 0.14336 0.14094 0.1551 0.19148 0.199 RANDOM 29.285
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] -0.13 -0.07 -0.13 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.508 r_sphericity_free 28.433 r_dihedral_angle_4_deg 18.444 r_dihedral_angle_3_deg 12.251 r_sphericity_bonded 11.194 r_rigid_bond_restr 8.681 r_dihedral_angle_1_deg 6.429 r_long_range_B_other 6.309 r_long_range_B_refined 6.306 r_scangle_other 5.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.508 r_sphericity_free 28.433 r_dihedral_angle_4_deg 18.444 r_dihedral_angle_3_deg 12.251 r_sphericity_bonded 11.194 r_rigid_bond_restr 8.681 r_dihedral_angle_1_deg 6.429 r_long_range_B_other 6.309 r_long_range_B_refined 6.306 r_scangle_other 5.661 r_scbond_it 4.465 r_scbond_other 4.412 r_mcangle_other 3.617 r_mcangle_it 3.616 r_angle_other_deg 3.503 r_mcbond_other 2.713 r_mcbond_it 2.701 r_angle_refined_deg 1.523 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1397 Nucleic Acid Atoms 164 Solvent Atoms 137 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing