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Loop deletion mutant of Salmonella typhi osmoporin (OmpC):an Outer Membrane Protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JN1 PDB ENTRY 2JN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.1 298.15 20% Polyethylene glycol 3350, 0.2M Calcium chloride dihydrate, pH 5.1, Microbatch, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 5.56 77.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.149 α = 90 b = 115.149 β = 90 c = 216.736 γ = 120
Symmetry Space Group P 63 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 77.03 CCD MARMOSAIC 225 mm CCD 2009-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97869 ESRF BM14
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 3.2 108.37 99.1 0.144 15.21 11.5 14709 14582
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 3.2 3.31 97.2 0.455 2.25 5.8
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 (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 2JN1 3.2 50 14709 13846 730 99.14 0.28953 0.28772 0.2835 0.32456 0.3244 RANDOM 91.449
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] 5.28 2.64 5.28 -7.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.073 r_dihedral_angle_4_deg 24.824 r_dihedral_angle_3_deg 24.267 r_dihedral_angle_1_deg 9.818 r_scangle_it 2.56 r_angle_refined_deg 1.701 r_scbond_it 1.502 r_mcangle_it 1.493 r_mcbond_it 0.792 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.073 r_dihedral_angle_4_deg 24.824 r_dihedral_angle_3_deg 24.267 r_dihedral_angle_1_deg 9.818 r_scangle_it 2.56 r_angle_refined_deg 1.701 r_scbond_it 1.502 r_mcangle_it 1.493 r_mcbond_it 0.792 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2406 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling