5MLE

Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293(0.2M magnesium chloride, 25% PEG 3350 and 0.1M bis-tris buffer pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9458.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.9α = 90
b = 185.82β = 90
c = 196.31γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4883.9899.920.9896.216.846370

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 REPLACEMENTTHROUGHOUT2GSE2.4883.9844041232899.940.208510.206010.25408RANDOM39.954
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]
0.04-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.58
r_dihedral_angle_4_deg20.298
r_dihedral_angle_3_deg17.308
r_long_range_B_refined7.871
r_long_range_B_other7.871
r_dihedral_angle_1_deg6.482
r_scangle_other4.234
r_mcangle_other3.795
r_mcangle_it3.792
r_scbond_it2.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.58
r_dihedral_angle_4_deg20.298
r_dihedral_angle_3_deg17.308
r_long_range_B_refined7.871
r_long_range_B_other7.871
r_dihedral_angle_1_deg6.482
r_scangle_other4.234
r_mcangle_other3.795
r_mcangle_it3.792
r_scbond_it2.591
r_scbond_other2.589
r_mcbond_it2.392
r_mcbond_other2.369
r_angle_refined_deg1.667
r_angle_other_deg1.042
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms7206
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing