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Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X5S PDB ENTRY 2X5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 200 MM CALCIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.926 α = 90 b = 79.567 β = 107.75 c = 70.952 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 ADSC CCD 2009-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 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 2.8 67.6 98.9 0.06 16 3.1 17147 3 66.9
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 2.8 2.95 99.1 0.48 2.6 3.1
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 2X5S 2.8 67.57 16126 1007 98.72 0.21104 0.20737 0.2431 0.26697 0.2904 RANDOM 74.769
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] 0.59 3.16 3.56 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_4_deg 15.414 r_dihedral_angle_1_deg 5.934 r_scangle_it 1.462 r_angle_refined_deg 1.218 r_scbond_it 0.857 r_angle_other_deg 0.813 r_mcangle_it 0.533 r_mcbond_it 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_4_deg 15.414 r_dihedral_angle_1_deg 5.934 r_scangle_it 1.462 r_angle_refined_deg 1.218 r_scbond_it 0.857 r_angle_other_deg 0.813 r_mcangle_it 0.533 r_mcbond_it 0.279 r_chiral_restr 0.068 r_mcbond_other 0.049 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 5380 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing