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Crystal structure of a BenF-like porin from Pseudomonas fluorescens Pf-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QTK Poly-Alanine model of the PDB code 2QTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100mM Citric acid, 21% PEG 3350, 10% w/v ANAPOE-X-114 from the detergent screen, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.103 α = 90 b = 210.624 β = 97.76 c = 84.066 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2009-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-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 2.58 53.68 100 0.14 6.1 3.9 67053 42.14
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) 2.58 2.72 100 0.527 2.7 3.8 9774
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 Poly-Alanine model of the PDB code 2QTK 2.58 35.11 66977 3390 100 0.222 0.22 0.2305 0.275 0.2793 RANDOM 41.96
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] 0.04 -0.02 -0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.064 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 7.22 r_scangle_it 2.202 r_angle_refined_deg 1.6 r_scbond_it 1.551 r_mcangle_it 1.26 r_angle_other_deg 0.95 r_mcbond_it 0.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.064 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 7.22 r_scangle_it 2.202 r_angle_refined_deg 1.6 r_scbond_it 1.551 r_mcangle_it 1.26 r_angle_other_deg 0.95 r_mcbond_it 0.737 r_symmetry_vdw_other 0.247 r_nbd_other 0.206 r_nbd_refined 0.191 r_nbtor_refined 0.184 r_mcbond_other 0.162 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.094 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11859 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 32
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling