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Crystal structure of the outer membrane enzyme PagL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4T Alanine model of NspA (1P4T) lacking the loops and turns.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 3000, glycerol, calcium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.264 α = 90 b = 48.993 β = 115.46 c = 105.026 γ = 90
Symmetry Space Group C 1 2 1
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 4 2004-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9793 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 30 90.3 0.051 0.051 20.9 3.1 28914 26464 -999 -3.7 29.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 52.2 52.2 0.38 0.38 3 2.7 1027
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT Alanine model of NspA (1P4T) lacking the loops and turns. 2 30 28914 26283 1336 90.9 0.2 0.2 0.198 0.1991 0.233 0.2345 RANDOM 28.04
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] -0.05 0.36 0.19 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 23.876 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.579 r_scangle_it 3.865 r_scbond_it 2.869 r_mcangle_it 1.803 r_angle_refined_deg 1.657 r_mcbond_it 1.136 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 23.876 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.579 r_scangle_it 3.865 r_scbond_it 2.869 r_mcangle_it 1.803 r_angle_refined_deg 1.657 r_mcbond_it 1.136 r_nbtor_refined 0.313 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.157 r_chiral_restr 0.139 r_symmetry_hbond_refined 0.121 r_metal_ion_refined 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2261 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 136
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction