5MKV

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2M ammonium acetate, 30% PEG 4000 and 0.1M citrate buffer pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.4950.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.9α = 90
b = 157.51β = 93.61
c = 87.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.819.8797.7115.843.6194435

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 REPLACEMENTTHROUGHOUT2GSE1.819.87184609971797.710.16820.166540.19963RANDOM25.454
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.456
r_dihedral_angle_4_deg18.956
r_dihedral_angle_3_deg13.38
r_dihedral_angle_1_deg6.224
r_long_range_B_refined5.47
r_long_range_B_other5.469
r_scangle_other4.553
r_scbond_it3.176
r_scbond_other3.174
r_mcangle_it3.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.456
r_dihedral_angle_4_deg18.956
r_dihedral_angle_3_deg13.38
r_dihedral_angle_1_deg6.224
r_long_range_B_refined5.47
r_long_range_B_other5.469
r_scangle_other4.553
r_scbond_it3.176
r_scbond_other3.174
r_mcangle_it3.046
r_mcangle_other3.046
r_mcbond_it2.283
r_mcbond_other2.279
r_angle_refined_deg1.952
r_angle_other_deg1.107
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.01
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 Atoms14957
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing