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Crystal structure of T. maritima GDP-mannose pyrophosphorylase in apo state.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CU2 PDB ENTRY 2CU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 100 MM PCB PH 7.5, 35% (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.011 α = 90 b = 92.999 β = 110.25 c = 69.687 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 2007-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.35 65.37 99.2 0.055 23.5 6 31744 3.5 59.338
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 2.35 2.48 96.9 0.47 2.5 5.4
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 2CU2 2.35 65.37 30129 1602 99.13 0.22648 0.22385 0.2476 0.27315 0.2793 RANDOM 75.786
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] -4.18 1.18 4.94 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.133 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_4_deg 14.452 r_dihedral_angle_1_deg 5.911 r_scangle_it 2.008 r_scbond_it 1.217 r_angle_refined_deg 1.154 r_mcangle_it 0.797 r_angle_other_deg 0.787 r_mcbond_it 0.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.133 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_4_deg 14.452 r_dihedral_angle_1_deg 5.911 r_scangle_it 2.008 r_scbond_it 1.217 r_angle_refined_deg 1.154 r_mcangle_it 0.797 r_angle_other_deg 0.787 r_mcbond_it 0.416 r_mcbond_other 0.073 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 5367 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing