2FUE

Human alpha-Phosphomannomutase 1 with D-mannose 1-phosphate and Mg2+ cofactor bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FUCpdb entry 2FUC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Crystals 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 coefficientSolvent content
2.3747.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.39α = 90
b = 51.39β = 90
c = 214.603γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.100NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.755094.80.0542.413.72873528735
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8175.50.455410.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 2FUC1.7524.228694272301464950.204220.202380.24033RANDOM27.633
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]
1.131.13-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.57
r_dihedral_angle_4_deg12.796
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg5.673
r_scangle_it1.849
r_scbond_it1.338
r_angle_refined_deg1.12
r_angle_other_deg0.813
r_mcangle_it0.731
r_mcbond_it0.648
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.57
r_dihedral_angle_4_deg12.796
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg5.673
r_scangle_it1.849
r_scbond_it1.338
r_angle_refined_deg1.12
r_angle_other_deg0.813
r_mcangle_it0.731
r_mcbond_it0.648
r_symmetry_vdw_other0.321
r_nbd_refined0.209
r_nbd_other0.196
r_nbtor_refined0.179
r_symmetry_vdw_refined0.156
r_symmetry_hbond_refined0.14
r_mcbond_other0.12
r_xyhbond_nbd_refined0.11
r_nbtor_other0.084
r_chiral_restr0.067
r_bond_refined_d0.008
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1973
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms18

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building