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Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IU8 PDB ENTRY 2IU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN INCUBATED WITH 100MM UDPGLCNAC AND CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% DIOXANE, 1MM TCEP, AND 2MM UDPGLCNAC.
Crystal Properties Matthews coefficient Solvent content 2.99 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.871 α = 90 b = 98.872 β = 90 c = 283.053 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE RIGAKU R-AXIS IV OSMIC MIRRORS 2004-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 3.1 28.5 98.9 0.15 11.1 5.1 26254
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 3.1 3.19 99.9 0.79 2.1 5.2
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 2IU8 3.1 28.5 24769 1323 99 0.224 0.221 0.2793 0.281 0.3237 RANDOM 76.21
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] 3.87 3.87 -7.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_4_deg 14.811 r_dihedral_angle_1_deg 5.183 r_angle_refined_deg 1.039 r_scangle_it 0.692 r_scbond_it 0.402 r_mcangle_it 0.342 r_nbtor_refined 0.301 r_mcbond_it 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_4_deg 14.811 r_dihedral_angle_1_deg 5.183 r_angle_refined_deg 1.039 r_scangle_it 0.692 r_scbond_it 0.402 r_mcangle_it 0.342 r_nbtor_refined 0.301 r_mcbond_it 0.193 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 7911 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling