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Human alpha-Phosphomannomutase 1 with D-mannose 1-phosphate and Mg2+ cofactor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FUC pdb entry 2FUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Crystals grown by hanging drop vapor diffusion over mother liquor containing 15-18% polyethylene glycol 3350, 0.15M D,L-malic acid, pH 7.0, 50mM MgCL2, and 8mM 2-mercaptoethanol. Drops were formed by mixing 2ul of protein solution (10mM HEPES, pH 7.5, 100mM NaCl, 5mM MgCl2) at 15-25mg/ml with 2ul of mother liquor. Crystals grew after one to three days at 296 K.
Crystal Properties Matthews coefficient Solvent content 2.37 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.39 α = 90 b = 51.39 β = 90 c = 214.603 γ = 90
Symmetry Space Group P 43 21 2
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 2005-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.100 NSLS X12C
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 1.75 50 94.8 0.05 42.4 13.7 28735 28735
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 1.75 1.81 75.5 0.455 4 10.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 2FUC 1.75 24.2 28694 27230 1464 95 0.20422 0.20238 0.2097 0.24033 0.2483 RANDOM 27.633
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] 1.13 1.13 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 12.796 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 5.673 r_scangle_it 1.849 r_scbond_it 1.338 r_angle_refined_deg 1.12 r_angle_other_deg 0.813 r_mcangle_it 0.731 r_mcbond_it 0.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 12.796 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 5.673 r_scangle_it 1.849 r_scbond_it 1.338 r_angle_refined_deg 1.12 r_angle_other_deg 0.813 r_mcangle_it 0.731 r_mcbond_it 0.648 r_symmetry_vdw_other 0.321 r_nbd_refined 0.209 r_nbd_other 0.196 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.14 r_mcbond_other 0.12 r_xyhbond_nbd_refined 0.11 r_nbtor_other 0.084 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1973 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building