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Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCI PDB ENTRY 2XCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL); SOAKING CRYSTALS IN 100 MM TRIS-HCL (PH 8.5), 36% (V/V) PEG 400, 200 MM NA-CITRATE AND 10 MM CMP FOR FOUR DAYS
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.77 α = 90 b = 44.67 β = 97.15 c = 143.64 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH SX-165 2009-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.42 31.85 97.2 0.04 21.3 3.6 62789 2 47.57
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 2.42 2.55 88.3 0.14 6.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2XCI 2.42 31.22 59636 3139 97.22 0.20478 0.20236 0.2003 0.25087 0.248 RANDOM 29.993
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] -2.6 -0.3 6.95 -4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.343 r_dihedral_angle_4_deg 19.815 r_dihedral_angle_3_deg 17.634 r_dihedral_angle_1_deg 6.555 r_scangle_it 3.501 r_scbond_it 2.027 r_angle_refined_deg 1.587 r_mcangle_it 1.407 r_mcbond_it 0.722 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.343 r_dihedral_angle_4_deg 19.815 r_dihedral_angle_3_deg 17.634 r_dihedral_angle_1_deg 6.555 r_scangle_it 3.501 r_scbond_it 2.027 r_angle_refined_deg 1.587 r_mcangle_it 1.407 r_mcbond_it 0.722 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11488 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing