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Crystal Structure of E. coli LsrF in complex with Ribulose-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 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.741 α = 90 b = 107.102 β = 102.62 c = 169.516 γ = 90
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 Si(111) 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 2.9 49.03 93 0.09 8.666 1.7 111445 111445
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 2.9 3 82.1 0.436 1.6 9821
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 (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 2.9 49.03 107205 107205 5678 94.24 0.197 0.195 0.2069 0.228 0.2238 RANDOM 25.53
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] 0.84 0.17 2.96 -2.03 0.54 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.664 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_4_deg 10.618 r_scangle_it 7.259 r_dihedral_angle_1_deg 4.803 r_scbond_it 4.135 r_mcangle_it 2.087 r_angle_refined_deg 1.178 r_mcbond_it 0.914 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.664 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_4_deg 10.618 r_scangle_it 7.259 r_dihedral_angle_1_deg 4.803 r_scbond_it 4.135 r_mcangle_it 2.087 r_angle_refined_deg 1.178 r_mcbond_it 0.914 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42260 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 280
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection