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Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 HEPES, PEG 4000, magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.723 α = 90 b = 72.471 β = 90 c = 82.728 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 CCD ADSC QUANTUM 4 2001-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 2.6 39.84 99.1 0.066 7.8 4.2 8506 8506 1.6 70
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 2.6 2.74 99.4 0.475 1.6 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.6 81.65 8721 8721 475 98.84 0.173 0.169 0.2635 0.251 0.3219 RANDOM 36.35
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] 2.32 -5.65 3.33
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.59 r_angle_refined_deg 2.093 p_mcangle_it 1.525 p_scbond_it 1.525 p_mcbond_it 0.871 r_bond_refined_d 0.023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2287 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 54
Software Software Software Name Purpose SOLVE phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling