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Structure of small-molecule inhibitor of Glmu from Haemophilus influenzae reveals an allosteric binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V0H PDB ENTRY 2V0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 1.7-1.8 M AMMONIUM SULFATE, 2% PEG-400, AND 0.1M MES PH 5.4-6.1
Crystal Properties Matthews coefficient Solvent content 3.46 64.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.186 α = 90 b = 108.186 β = 90 c = 327.43 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 ADSC CCD 2004-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 1.9 20 94.4 0.06 22 5.3 55305
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 1.9 1.97 84.5 0.25 4.8 4.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V0H 1.9 111.8 52488 1 90 0.183 0.182 0.1923 0.204 RANDOM 20.38
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] 0.56 0.28 0.56 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.838 r_scangle_it 2.322 r_mcangle_it 1.76 r_scbond_it 1.405 r_angle_refined_deg 1.27 r_mcbond_it 1.061 r_angle_other_deg 0.931 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.838 r_scangle_it 2.322 r_mcangle_it 1.76 r_scbond_it 1.405 r_angle_refined_deg 1.27 r_mcbond_it 1.061 r_angle_other_deg 0.931 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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 3414 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 97
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling CNX phasing REFMAC phasing REFMAC refinement