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GDP-mannose mannosyl hydrolase-calcium-GDP-mannose complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 281 10-20% PEG 4000
200 mM sodium acetate
100 mM HEPES, pH 8.0
harvested immediately after growth, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.57 52.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.636 α = 90 b = 81.586 β = 90 c = 98.3 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 MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.3 50 95.8 0.04 29 4 94585 1
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 1.3 1.35 81.2 0.149 4 7936
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.3 42.41 94526 6806 100 0.153 0.153 0.151 0.174 RANDOM 8.43
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] 0.29 -0.09 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.391 r_sphericity_free 19.806 r_dihedral_angle_4_deg 13.54 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 4.82 r_sphericity_bonded 1.705 r_angle_refined_deg 1.703 r_scangle_it 1.586 r_mcangle_it 1.298 r_scbond_it 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.391 r_sphericity_free 19.806 r_dihedral_angle_4_deg 13.54 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 4.82 r_sphericity_bonded 1.705 r_angle_refined_deg 1.703 r_scangle_it 1.586 r_mcangle_it 1.298 r_scbond_it 1.112 r_angle_other_deg 1.035 r_mcbond_it 0.875 r_rigid_bond_restr 0.469 r_symmetry_vdw_other 0.357 r_nbd_other 0.192 r_nbd_refined 0.186 r_nbtor_refined 0.186 r_mcbond_other 0.146 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.138 r_metal_ion_refined 0.114 r_symmetry_vdw_refined 0.098 r_chiral_restr 0.095 r_nbtor_other 0.083 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2448 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 92
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling