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Structure of UDP-galactopyranose mutase bound to flavin mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GF4 PDB ENTRY 3GF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 DROPS CONTAINING 1.5 MICROLITERS 5 MG/ML PROTEIN IN 20 MM HEPES PH 7.0 WERE COMBINED WITH 1.5 MICROLITERS WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI-SODIUM CITRATE, 12.3% PEG 4000, 7.5% GLYCEROL, 15 MM L-CYSTEINE, 5 MM UDP-GLC) FOR 1-2 WEEKS. CRYSTAL WAS THEN SOAKED IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS AND 23 MM FLAVIN MONONUCLEOTIDE (24HRS). CRYSTAL WAS BRIEFLY SOAKED (20 SECONDS) IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, 10 MM FLAVIN MONONUCLEOTIDE PRIOR TO VITRIFICATION, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.8 α = 90 b = 93.8 β = 90 c = 128.8 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 MARMOSAIC 300 mm CCD beryllium lens 2008-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 50 100 0.093 17 7.6 49496 49472 39.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 100 0.286 7.2 7.3 4912
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 3GF4 2.3 30 46879 46820 2499 99.87 0.185 0.185 0.183 0.1787 0.221 0.2136 RANDOM 32.6
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] -0.71 -0.71 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.137 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 16.464 r_dihedral_angle_1_deg 6.697 r_scangle_it 5.403 r_scbond_it 3.469 r_mcangle_it 2.215 r_angle_refined_deg 2.007 r_mcbond_it 1.229 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.137 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 16.464 r_dihedral_angle_1_deg 6.697 r_scangle_it 5.403 r_scbond_it 3.469 r_mcangle_it 2.215 r_angle_refined_deg 2.007 r_mcbond_it 1.229 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6227 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 230
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling