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Crystal structure of PagP in SDS/MPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1THQ PDB entry 1THQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 1M MPD, 0.1M citrate pH 5.6, 1.7M lithium sulphate, 0.3M ammonium sulphate, SDS, Phase separation, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.228 α = 90 b = 113.228 β = 90 c = 55.064 γ = 120
Symmetry Space Group P 62 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 315 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 20 97.7 0.068 8.2 40433 40433 -3 -3 21.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.42 80.4 0.531 1.36 4.1 1633
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1THQ 1.4 20 -3 -3 39132 39132 1260 97.74 0.17259 0.17259 0.17147 0.1736 0.20817 0.2132 RANDOM 28.065
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] 3.2 1.6 3.2 -4.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 18.014 r_sphericity_free 15.265 r_dihedral_angle_3_deg 13.991 r_sphericity_bonded 9.638 r_dihedral_angle_1_deg 7.084 r_scangle_it 5.134 r_scbond_it 4.125 r_mcangle_it 3.806 r_mcbond_it 2.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 18.014 r_sphericity_free 15.265 r_dihedral_angle_3_deg 13.991 r_sphericity_bonded 9.638 r_dihedral_angle_1_deg 7.084 r_scangle_it 5.134 r_scbond_it 4.125 r_mcangle_it 3.806 r_mcbond_it 2.793 r_rigid_bond_restr 2.612 r_angle_refined_deg 2.119 r_mcbond_other 1.726 r_angle_other_deg 0.96 r_xyhbond_nbd_refined 0.244 r_symmetry_vdw_other 0.242 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.222 r_metal_ion_refined 0.217 r_nbtor_refined 0.199 r_nbd_other 0.193 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.137 r_symmetry_metal_ion_refined 0.105 r_nbtor_other 0.092 r_xyhbond_nbd_other 0.042 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1258 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 209
Software Software Software Name Purpose HKL-3000 data collection EPMR phasing REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling