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Structure of E.coli FabD complexed with glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MLA
Crystallization Crystal Properties Matthews coefficient Solvent content 4.4 72.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.147 α = 90 b = 83.147 β = 90 c = 164.511 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 100 IMAGE PLATE MARRESEARCH mirrors 2001-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 1.86 20 97.5 0.061 44.7 48061 48061 2.1 2.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.98 99.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1MLA 1.86 20 45525 45525 2436 97.41 0.2111 0.21111 0.21052 0.2228 0.22213 0.2347 RANDOM 26.493
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] 0.22 0.22 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.386 r_dihedral_angle_1_deg 7.243 r_scangle_it 3.762 r_mcangle_it 2.877 r_scbond_it 2.449 r_mcbond_it 1.86 r_angle_refined_deg 0.754 r_symmetry_hbond_refined 0.712 r_angle_other_deg 0.58 r_symmetry_vdw_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.386 r_dihedral_angle_1_deg 7.243 r_scangle_it 3.762 r_mcangle_it 2.877 r_scbond_it 2.449 r_mcbond_it 1.86 r_angle_refined_deg 0.754 r_symmetry_hbond_refined 0.712 r_angle_other_deg 0.58 r_symmetry_vdw_refined 0.335 r_nbd_refined 0.309 r_xyhbond_nbd_other 0.272 r_nbd_other 0.25 r_xyhbond_nbd_refined 0.227 r_symmetry_vdw_other 0.225 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2257 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing