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GDP-mannose mannosyl hydrolase-calcium-GDP product 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 72 hours after growth, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.588 α = 90 b = 81.151 β = 90 c = 97.982 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 IMAGE PLATE MAR scanner 180 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 50 98.7 0.041 18.5 4.8 77746
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) 1.4 1.45 96.4 0.1 4.6 7466
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 1.4 38.84 77674 5598 100 0.142 0.142 0.14 0.164 RANDOM 8.697
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] 0.31 -0.02 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.224 r_sphericity_free 20.924 r_dihedral_angle_4_deg 12.929 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_1_deg 4.889 r_sphericity_bonded 1.841 r_scangle_it 1.686 r_angle_refined_deg 1.653 r_mcangle_it 1.413 r_scbond_it 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.224 r_sphericity_free 20.924 r_dihedral_angle_4_deg 12.929 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_1_deg 4.889 r_sphericity_bonded 1.841 r_scangle_it 1.686 r_angle_refined_deg 1.653 r_mcangle_it 1.413 r_scbond_it 1.159 r_angle_other_deg 1.049 r_mcbond_it 0.928 r_rigid_bond_restr 0.483 r_symmetry_vdw_other 0.373 r_nbd_other 0.197 r_nbd_refined 0.187 r_nbtor_refined 0.186 r_mcbond_other 0.15 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.141 r_metal_ion_refined 0.131 r_symmetry_vdw_refined 0.102 r_chiral_restr 0.094 r_nbtor_other 0.084 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 557 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing