5M3U

The X-ray structure of human V216F phosphoglycerate kinase 1 mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZGV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2982.2-2.5 M NAKPO4, PH 8.2-8.4,
Crystal Properties
Matthews coefficientSolvent content
2.0238.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.65α = 90
b = 106.031β = 98.71
c = 50.097γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2016-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.8150960.080.99711.224.532377
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.9279.10.560.7531.883.84

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 REPLACEMENTTHROUGHOUT2ZGV1.815030810153996.190.194420.1920.24159RANDOM30.912
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]
0.32-0.12-0.02-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.782
r_dihedral_angle_4_deg17.689
r_dihedral_angle_3_deg14.745
r_dihedral_angle_1_deg6.708
r_long_range_B_refined5.933
r_long_range_B_other5.922
r_scangle_other4.358
r_mcangle_it3.391
r_mcangle_other3.39
r_scbond_it2.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.782
r_dihedral_angle_4_deg17.689
r_dihedral_angle_3_deg14.745
r_dihedral_angle_1_deg6.708
r_long_range_B_refined5.933
r_long_range_B_other5.922
r_scangle_other4.358
r_mcangle_it3.391
r_mcangle_other3.39
r_scbond_it2.806
r_scbond_other2.788
r_mcbond_it2.321
r_mcbond_other2.321
r_angle_refined_deg1.735
r_angle_other_deg0.992
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms3120
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing