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Crystal structure of H10N mutant of LpxH
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 7 293 0.2M Proline, 0.1M HEPES pH 7.0, 10.0% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.564 α = 90 b = 87.888 β = 90 c = 98.358 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 CCD RAYONIX MX225HE 2011-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 1.75 50 99.8 0.078 18.4 4.9 59677
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 1.75 1.81 100 0.551 2.13 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 1.75 49.18 56369 2991 99.39 0.17949 0.17831 0.1853 0.2015 0.2073 RANDOM 27.679
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] 0.07 -0.3 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.293 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 12.642 r_long_range_B_refined 7.858 r_long_range_B_other 7.681 r_scangle_other 6.059 r_dihedral_angle_1_deg 5.439 r_scbond_it 3.997 r_scbond_other 3.992 r_mcangle_it 3.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.293 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 12.642 r_long_range_B_refined 7.858 r_long_range_B_other 7.681 r_scangle_other 6.059 r_dihedral_angle_1_deg 5.439 r_scbond_it 3.997 r_scbond_other 3.992 r_mcangle_it 3.195 r_mcangle_other 3.195 r_mcbond_it 2.406 r_mcbond_other 2.406 r_angle_refined_deg 1.464 r_angle_other_deg 0.991 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 3752 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing