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The Structure of the inactive mutant G153R of LptC from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MY2 PDB ENTRY 3MY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 STURA FOOTPRINT SCREEN NUMBER 1 CONDITION 18.2 (MOLECULAR DIMENSIONS) 18% PEG5K MME, 0.1M SODIUM ACETATE PH 5.5 PLUS 30% GLYCEROL FOR CRYOCOOLING
Crystal Properties Matthews coefficient Solvent content 2.3 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.94 α = 90 b = 98.28 β = 90 c = 123.56 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2010-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.8 40 99.5 0.12 12.9 5.1 12846 2
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 2.8 2.95 99.4 0.72 3.2 5.4
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 PDB ENTRY 3MY2 2.8 40 12169 621 99.12 0.24155 0.24035 0.238 0.26551 0.2587 RANDOM 60.04
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] 2.35 -1.61 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_dihedral_angle_4_deg 18.198 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 4.816 r_mcangle_it 1.014 r_angle_refined_deg 0.914 r_scangle_it 0.812 r_mcbond_it 0.563 r_scbond_it 0.492 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_dihedral_angle_4_deg 18.198 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 4.816 r_mcangle_it 1.014 r_angle_refined_deg 0.914 r_scangle_it 0.812 r_mcbond_it 0.563 r_scbond_it 0.492 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2033 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing