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Crystal structure of DnaD-like replication protein from Streptococcus mutans UA159, gi 24377835, residues 127-199
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 20% v/v 1,4-butanediol, 0.1M Imidazole, 0.2M Zinc acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.701 α = 90 b = 81.701 β = 90 c = 52.464 γ = 90
Symmetry Space Group P 41 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 315 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 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 50 99.2 0.06 11.7 8.8 22797 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) 2 2.02 93 0.527 5.3 559
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.1 40.86 10802 518 99.79 0.246 0.243 0.288 0.2793 RANDOM 24.874
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] 0.64 0.64 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.702 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 17.972 r_scangle_it 5.72 r_dihedral_angle_1_deg 5.418 r_scbond_it 3.702 r_mcangle_it 2.227 r_angle_refined_deg 1.72 r_mcbond_it 1.428 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.702 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 17.972 r_scangle_it 5.72 r_dihedral_angle_1_deg 5.418 r_scbond_it 3.702 r_mcangle_it 2.227 r_angle_refined_deg 1.72 r_mcbond_it 1.428 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.292 r_symmetry_hbond_refined 0.278 r_symmetry_metal_ion_refined 0.227 r_nbd_refined 0.222 r_metal_ion_refined 0.178 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1252 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection