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Crystal Structure of E. coli LsrF in complex with Ribose-5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GKF PDB entry 3GKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 4% PEG 400, 100 mM MgCl2, 2.3 M Ammonium Sulfate, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.352 α = 89.51 b = 105.451 β = 79.79 c = 173.415 γ = 90.34
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 QUANTUM 4 2008-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.00 NSLS X26C
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 2.5 55.73 81.7 0.065 7.5 2.1 327170 154484 45.3
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 2.5 2.64 67.8 0.279 1.8 1.7 18764
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 PDB entry 3GKF 2.5 55.73 127454 127454 6338 67.42 0.206 0.206 0.205 0.1994 0.235 0.2284 RANDOM 35.975
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] -2.42 -1.47 -0.47 1.71 2.8 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.896 r_dihedral_angle_4_deg 15.075 r_dihedral_angle_3_deg 14.675 r_scangle_it 6.004 r_dihedral_angle_1_deg 5.579 r_scbond_it 3.239 r_mcangle_it 1.802 r_angle_refined_deg 1.358 r_mcbond_it 0.837 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.896 r_dihedral_angle_4_deg 15.075 r_dihedral_angle_3_deg 14.675 r_scangle_it 6.004 r_dihedral_angle_1_deg 5.579 r_scbond_it 3.239 r_mcangle_it 1.802 r_angle_refined_deg 1.358 r_mcbond_it 0.837 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42260 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 280
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection