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Structure of LpxC from Aquifex aeolicus in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P42 PDB ENTRY 1P42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 CRYSTALS OF LPXC WERE GROWN BY HANGING VAPOR DIFFUSION AT 20 DEG C USING 1 UL OF PROTEIN (184 UM) AND 1 UL OF A RESERVOIR SOLUTION CONTAINING 8% PEG 6000, 100 MM TRIS, PH 8.5, AND 300 MM NACL.
Crystal Properties Matthews coefficient Solvent content 2.69 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.755 α = 90 b = 101.755 β = 90 c = 124.243 γ = 120
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 MARRESEARCH PT-COATED MIRRORS, MICROFOCUS BEAMLINE 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.2 50.9 99 0.11 11.3 3.9 36577
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 2.2 2.32 98.5 0.48 3.6 3.9
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 1P42 2.2 50.9 34736 1836 98.9 0.171 0.168 0.1659 0.225 0.2219 RANDOM 22.83
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] -0.86 -0.43 -0.86 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_1_deg 5.973 r_scangle_it 2.701 r_scbond_it 1.671 r_angle_refined_deg 1.34 r_mcangle_it 1.058 r_mcbond_it 0.653 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_1_deg 5.973 r_scangle_it 2.701 r_scbond_it 1.671 r_angle_refined_deg 1.34 r_mcangle_it 1.058 r_mcbond_it 0.653 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.199 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.105 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4314 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing