5MUF

Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MXO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.729318% PEG 3350 and 0.1 M MES, pH 5.7
Crystal Properties
Matthews coefficientSolvent content
3.2762.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.215α = 90
b = 141.403β = 90
c = 183.12γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2011-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
13.141.0394.30.2710.1016.871824355.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2796.20.9930.37326.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3MXO3.141.031730093392.40.227930.226480.25553RANDOM50.597
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]
0.491.02-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.083
r_dihedral_angle_3_deg15.347
r_dihedral_angle_4_deg13.027
r_dihedral_angle_1_deg6.308
r_long_range_B_refined2.385
r_long_range_B_other2.385
r_mcangle_it1.156
r_mcangle_other1.156
r_angle_refined_deg1.104
r_scangle_other0.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.083
r_dihedral_angle_3_deg15.347
r_dihedral_angle_4_deg13.027
r_dihedral_angle_1_deg6.308
r_long_range_B_refined2.385
r_long_range_B_other2.385
r_mcangle_it1.156
r_mcangle_other1.156
r_angle_refined_deg1.104
r_scangle_other0.881
r_angle_other_deg0.779
r_mcbond_it0.623
r_mcbond_other0.623
r_scbond_it0.466
r_scbond_other0.462
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5062
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing