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Crystal structure of E. coli TdcF with bound propionate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QU9 PDB ENTRY 1QU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.02 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.435 α = 90 b = 85.744 β = 90 c = 62.512 γ = 90
Symmetry Space Group P 21 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 OSMIC CONFOCAL MIRRORS 2002-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.45 25.25 98.9 0.08 12.49 3.4 14818 35.93
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 2.45 2.54 94 0.3 2.58
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 1QU9 2.44 24.58 14817 756 99.2 0.171 0.166 0.1625 0.253 0.2498 RANDOM 21.23
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] -1.007 0.8 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_dihedral_angle_4_deg 22.264 r_dihedral_angle_3_deg 17.594 r_dihedral_angle_1_deg 7.077 r_scangle_it 4.329 r_scbond_it 2.766 r_angle_refined_deg 1.843 r_mcangle_it 1.79 r_mcbond_it 1.122 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_dihedral_angle_4_deg 22.264 r_dihedral_angle_3_deg 17.594 r_dihedral_angle_1_deg 7.077 r_scangle_it 4.329 r_scbond_it 2.766 r_angle_refined_deg 1.843 r_mcangle_it 1.79 r_mcbond_it 1.122 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.112 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 2860 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing