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Crystal structure of PpcA V13A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 3.7 M ammonium sulfate pH adjusted to 6.0 with ammonium hydroxide; 0.25% deoxycholate in the drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.2 α = 90 b = 32.2 β = 90 c = 178.8 γ = 90
Symmetry Space Group P 43 2 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 210r 2003-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.03320 APS 19-BM
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 1.9 90 94.5 0.04 58.1 5.9 7763 -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 1.9 1.97 73.8 0.087 16.1 2.4 554
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 1OS6 1.9 30 6920 752 94.19 0.192 0.18784 0.1845 0.22949 0.2263 RANDOM 16.277
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] 0.34 0.34 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.678 r_scangle_it 3.619 r_scbond_it 2.375 r_mcangle_it 1.897 r_angle_refined_deg 1.479 r_mcbond_it 0.969 r_angle_other_deg 0.912 r_nbd_refined 0.39 r_symmetry_hbond_refined 0.339 r_nbd_other 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.678 r_scangle_it 3.619 r_scbond_it 2.375 r_mcangle_it 1.897 r_angle_refined_deg 1.479 r_mcbond_it 0.969 r_angle_other_deg 0.912 r_nbd_refined 0.39 r_symmetry_hbond_refined 0.339 r_nbd_other 0.3 r_symmetry_vdw_other 0.285 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.137 r_nbtor_other 0.083 r_chiral_restr 0.075 r_metal_ion_refined 0.023 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 530 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing