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gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), k217a, with gdp-alpha-d-mannose bound in the active site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C54 PDB ENTRY 2C54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 100 MM BIS-TRIS PH 6.0, 2.2 M AMMONIUM SULPHATE. SITTING DROP, VAPOUR DIFFUSION. CRYOPTROTECTED WITH 6 M SODIUM FORMATE.
Crystal Properties Matthews coefficient Solvent content 1.75 29.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.481 α = 90 b = 83.617 β = 99.01 c = 66.232 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 2005-05-15 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 1.7 35.22 99.8 0.09 13.2 3.8 73777 15.5
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 1.7 1.79 99.7 0.44 2.2 3.8
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 2C54 1.7 34.61 73742 3705 99.8 0.134 0.131 0.1294 0.193 0.1917 RANDOM 16.41
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] -0.624 -0.273 1.25 -0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.171 r_dihedral_angle_4_deg 21.818 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.412 r_scbond_it 3.194 r_mcangle_it 2.079 r_angle_refined_deg 1.735 r_mcbond_it 1.556 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.171 r_dihedral_angle_4_deg 21.818 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.412 r_scbond_it 3.194 r_mcangle_it 2.079 r_angle_refined_deg 1.735 r_mcbond_it 1.556 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5776 Nucleic Acid Atoms Solvent Atoms 870 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling