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Human alpha-Phosphomannomutase 1 with Mg2+ cofactor bound
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 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.69 α = 90 b = 51.69 β = 90 c = 215.98 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 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9797, 0.9794, 0.9500 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 2.1 50 99 0.056 45.3 18.9 17978 17978
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) 2.1 2.18 99.9 0.405 8.8 16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2.1 24.33 15848 15848 868 100 0.18733 0.18629 0.20597 0.2371 RANDOM 30.054
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] 0.79 0.79 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_3_deg 13.253 r_dihedral_angle_4_deg 9.435 r_dihedral_angle_1_deg 6.144 r_scangle_it 1.608 r_mcangle_it 1.523 r_mcbond_it 1.395 r_scbond_it 1.187 r_angle_refined_deg 1.136 r_angle_other_deg 0.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_3_deg 13.253 r_dihedral_angle_4_deg 9.435 r_dihedral_angle_1_deg 6.144 r_scangle_it 1.608 r_mcangle_it 1.523 r_mcbond_it 1.395 r_scbond_it 1.187 r_angle_refined_deg 1.136 r_angle_other_deg 0.669 r_symmetry_vdw_other 0.347 r_nbd_refined 0.231 r_nbd_other 0.213 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.178 r_mcbond_other 0.171 r_metal_ion_refined 0.092 r_nbtor_other 0.088 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 1969 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SnB phasing