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Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O52 PDB entry 3O52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 20-26% PEG 3350, 0.2 M Mg Cl, 0.1 M Tris HCL pH 8.5, 4mM GDP-mannose at a ratio of 1:1 protein:reservoir, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.379 α = 90 b = 69.26 β = 90 c = 98.554 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944+ 2009-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54
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 22.81 96 0.089 12.8 5.6 23871
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) 2.1 2.18 75.1 0.331 3.3 1827
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3O52 2.1 22.81 23750 1200 95.85 0.2084 0.2048 0.2796 0.2408 RANDOM 24.7644
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] 0.68 -0.56 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.613 r_dihedral_angle_4_deg 16.378 r_dihedral_angle_3_deg 15.292 r_dihedral_angle_1_deg 6.334 r_scangle_it 2.924 r_scbond_it 1.797 r_angle_refined_deg 1.262 r_mcangle_it 1.226 r_angle_other_deg 1.16 r_mcbond_it 0.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.613 r_dihedral_angle_4_deg 16.378 r_dihedral_angle_3_deg 15.292 r_dihedral_angle_1_deg 6.334 r_scangle_it 2.924 r_scbond_it 1.797 r_angle_refined_deg 1.262 r_mcangle_it 1.226 r_angle_other_deg 1.16 r_mcbond_it 0.655 r_nbd_other 0.436 r_nbtor_refined 0.301 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.148 r_metal_ion_refined 0.129 r_chiral_restr 0.085 r_nbtor_other 0.07 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2932 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing