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Structure of the E. coli GDP-mannose mannosyl hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYA PDB ENTRY 1RYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.4M Potassium Sodium Tartrate tetra-hydrate, pH 0.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.767 α = 90 b = 48.767 β = 90 c = 210.23 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 210 2004-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
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 2 223.61 92.3 0.07 19.4 4.1 34871
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 63.8 0.206 0.206 4.03 1.8 2405
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RYA 2 223.61 34871 34871 1747 92.09 0.204 0.204 0.201 0.257 RANDOM 32.477
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] -0.35 -0.18 -0.35 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.287 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_1_deg 5.499 r_scangle_it 1.779 r_scbond_it 1.169 r_mcangle_it 1.06 r_angle_refined_deg 1.058 r_mcbond_it 0.598 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.287 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_1_deg 5.499 r_scangle_it 1.779 r_scbond_it 1.169 r_mcangle_it 1.06 r_angle_refined_deg 1.058 r_mcbond_it 0.598 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.183 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4937 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MADNESS data reduction AMoRE phasing