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GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose 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, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE.
Crystal Properties Matthews coefficient Solvent content 1.99 38.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.497 α = 90 b = 83.273 β = 98.89 c = 66.12 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 1.4 23.12 96.7 0.05 17.9 3.6 126826 11
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 1.4 1.48 95.4 0.23 5.5 3.5
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 1.4 21.61 126798 6337 96.5 0.105 0.103 0.1152 0.14 0.149 RANDOM 9.78
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] -0.262 -0.05 0.589 -0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.509 r_dihedral_angle_4_deg 21.328 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 6.407 r_scangle_it 4.774 r_scbond_it 3.673 r_mcangle_it 2.518 r_mcbond_it 2.188 r_angle_refined_deg 1.921 r_angle_other_deg 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.509 r_dihedral_angle_4_deg 21.328 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 6.407 r_scangle_it 4.774 r_scbond_it 3.673 r_mcangle_it 2.518 r_mcbond_it 2.188 r_angle_refined_deg 1.921 r_angle_other_deg 1.086 r_symmetry_vdw_other 0.283 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.227 r_symmetry_hbond_refined 0.225 r_chiral_restr 0.217 r_nbd_other 0.208 r_symmetry_vdw_refined 0.191 r_nbtor_refined 0.186 r_nbtor_other 0.089 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 5786 Nucleic Acid Atoms Solvent Atoms 1018 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling