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Crystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum in complex with L-Rhamnose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QLW PDB entry 2QLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 2M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.652 α = 90 b = 68.652 β = 90 c = 100.719 γ = 120
Symmetry Space Group P 32 1 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 MIRRORS 2006-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.85 30 98.3 0.093 4.2 23317 23317
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 1.85 1.92 92.5 0.322 3.7 2.8 2169
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 2QLW 2 28.51 18417 18417 942 99.04 0.138 0.138 0.135 0.1473 0.188 0.1927 RANDOM 16.591
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.064 r_dihedral_angle_4_deg 18.664 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_1_deg 5.452 r_scangle_it 4.393 r_scbond_it 3.093 r_angle_other_deg 1.86 r_mcangle_it 1.82 r_angle_refined_deg 1.777 r_mcbond_it 1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.064 r_dihedral_angle_4_deg 18.664 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_1_deg 5.452 r_scangle_it 4.393 r_scbond_it 3.093 r_angle_other_deg 1.86 r_mcangle_it 1.82 r_angle_refined_deg 1.777 r_mcbond_it 1.511 r_mcbond_other 0.341 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.238 r_nbd_other 0.21 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.144 r_nbtor_other 0.096 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1748 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOLREP phasing