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Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and 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 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.276 α = 90 b = 55.824 β = 91.71 c = 158.121 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 QUANTUM 210 2009-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9787 NSLS X6A
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 2.45 32.4 93 0.098 14.4 3.2 32636
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) 2.45 2.49 59 0.165 1.8 1030
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 2.45 32.4 32614 1644 92.73 0.2273 0.2239 0.2902 0.2914 RANDOM 53.14
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] -6.3 1.64 7.41 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.857 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_1_deg 6.714 r_scangle_it 2.627 r_scbond_it 1.697 r_angle_refined_deg 1.584 r_mcangle_it 1.052 r_mcbond_it 0.575 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.857 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_1_deg 6.714 r_scangle_it 2.627 r_scbond_it 1.697 r_angle_refined_deg 1.584 r_mcangle_it 1.052 r_mcbond_it 0.575 r_nbtor_refined 0.315 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.173 r_metal_ion_refined 0.136 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5971 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 163
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction