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Crystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum
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 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.241 α = 90 b = 69.241 β = 90 c = 101.106 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 MAR CCD 165 mm Mirrors 2006-02-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.9079 ESRF BM16
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 1.6 30 97.1 0.097 11.2 5.7 35978 35978
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 1.6 1.66 97 0.589 3.2 5.6 3574
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 (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 SAD THROUGHOUT 1.6 19.99 35783 35783 1786 97.15 0.153 0.153 0.152 0.1611 0.18 0.187 RANDOM 10.823
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] 0.08 0.04 0.08 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.346 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 5.396 r_scangle_it 4.535 r_scbond_it 3.27 r_mcangle_it 1.782 r_angle_other_deg 1.711 r_angle_refined_deg 1.69 r_mcbond_it 1.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.346 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 5.396 r_scangle_it 4.535 r_scbond_it 3.27 r_mcangle_it 1.782 r_angle_other_deg 1.711 r_angle_refined_deg 1.69 r_mcbond_it 1.519 r_mcbond_other 0.311 r_nbd_refined 0.227 r_nbd_other 0.214 r_symmetry_vdw_other 0.2 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.136 r_symmetry_hbond_refined 0.129 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1748 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection SHELXD phasing