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H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in complex with GDP-alpha-D-Mannose and Mg(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVL PDB ENTRY 2WVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 AS AN ADDITIVE, 1-5 MM GDP-ALPHA-D-MANNOSE
Crystal Properties Matthews coefficient Solvent content 3.6 65.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.766 α = 90 b = 112.766 β = 90 c = 199.69 γ = 90
Symmetry Space Group P 41 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.977 48.9 94 0.04 15.4 2.7 25598
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 2.977 3.16 80.6 0.37 2.09 2.1
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 2WVL 2.977 98.19 24263 1292 94.15 0.17643 0.17355 0.1732 0.23163 0.2325 RANDOM 55.868
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] 3.23 3.23 -6.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_4_deg 20.468 r_dihedral_angle_3_deg 19.749 r_dihedral_angle_1_deg 6.6 r_scangle_it 4.622 r_scbond_it 2.685 r_angle_refined_deg 1.642 r_mcangle_it 1.34 r_mcbond_it 0.656 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_4_deg 20.468 r_dihedral_angle_3_deg 19.749 r_dihedral_angle_1_deg 6.6 r_scangle_it 4.622 r_scbond_it 2.685 r_angle_refined_deg 1.642 r_mcangle_it 1.34 r_mcbond_it 0.656 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 5880 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing