☰ Navigation Tabs
Crystal structure of LpxH with lipid X in spacegroup C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 131mM DL-Malic acid pH7.0, 17.5% PEG 3350, 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.534 α = 90 b = 42.484 β = 125.12 c = 100.756 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 270 2010-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.6 50 99 0.073 18.3 5 65538
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 1.6 1.66 97 0.575 1.97 4.8
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 5B49 1.6 49.78 62089 3315 98.63 0.16241 0.16094 0.1747 0.19008 0.2009 RANDOM 20.004
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] 0.02 0.01 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 15.672 r_dihedral_angle_3_deg 12.25 r_long_range_B_refined 7.009 r_long_range_B_other 6.847 r_dihedral_angle_1_deg 5.436 r_scangle_other 5.365 r_scbond_it 3.504 r_scbond_other 3.503 r_mcangle_it 2.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 15.672 r_dihedral_angle_3_deg 12.25 r_long_range_B_refined 7.009 r_long_range_B_other 6.847 r_dihedral_angle_1_deg 5.436 r_scangle_other 5.365 r_scbond_it 3.504 r_scbond_other 3.503 r_mcangle_it 2.683 r_mcangle_other 2.682 r_mcbond_it 1.895 r_mcbond_other 1.886 r_angle_refined_deg 1.451 r_angle_other_deg 0.972 r_chiral_restr 0.056 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3891 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing