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Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris CGA009
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 297 0.1 M Tris-Cl, 1.5 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.215 α = 90 b = 44.33 β = 90 c = 75.81 γ = 90
Symmetry Space Group P 21 21 2
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 315r 2010-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2.05 50 99.6 0.079 42.5 7.1 23364 23262 -3 35.3
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 2.05 2.09 99.6 0.691 4.23 7 1131
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.05 43.77 22903 22903 1183 98.1 0.1869 0.1869 0.18444 0.1958 0.23182 0.2383 RANDOM 28.824
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] -0.43 0.2 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.572 r_dihedral_angle_4_deg 17.261 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_1_deg 5.023 r_scangle_it 3.952 r_scbond_it 2.327 r_angle_refined_deg 1.301 r_mcangle_it 1.25 r_mcbond_it 0.667 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.572 r_dihedral_angle_4_deg 17.261 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_1_deg 5.023 r_scangle_it 3.952 r_scbond_it 2.327 r_angle_refined_deg 1.301 r_mcangle_it 1.25 r_mcbond_it 0.667 r_chiral_restr 0.092 r_bond_refined_d 0.014 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 2569 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 10
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing