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Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with mannose-1-phosphate.
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 35% (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 2.4 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.933 α = 90 b = 91.738 β = 110.75 c = 69.73 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 2009-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 2.1 65.2 98.7 0.04 17.3 3.1 43388 3 36.3
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 2.1 2.21 98.8 0.47 2.5 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 2.1 65.21 42013 1352 98.56 0.18837 0.187 0.2214 0.2301 0.2447 RANDOM 50.16
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] -2.39 1.25 1.65 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.241 r_dihedral_angle_3_deg 15.593 r_dihedral_angle_4_deg 14.372 r_dihedral_angle_1_deg 6.163 r_scangle_it 2.773 r_scbond_it 1.754 r_angle_refined_deg 1.335 r_mcangle_it 1.101 r_angle_other_deg 0.843 r_mcbond_it 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.241 r_dihedral_angle_3_deg 15.593 r_dihedral_angle_4_deg 14.372 r_dihedral_angle_1_deg 6.163 r_scangle_it 2.773 r_scbond_it 1.754 r_angle_refined_deg 1.335 r_mcangle_it 1.101 r_angle_other_deg 0.843 r_mcbond_it 0.6 r_mcbond_other 0.135 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 5418 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing