3D42

Crystal structure of HePTP in complex with a monophosphorylated Erk2 peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.62770.2 M AMMONIUM TARTRATE DIBASIC, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.244.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.46α = 90
b = 39.035β = 124.59
c = 83.65γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210SI(III) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR2008-02-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.000NSLSX6A

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
12.455093.90.1112.91112910896124.9
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)
12.452.5490.60.2212.31048

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2QDM2.46202108311058552494.330.2160.184140.18130.24082RANDOM15.91
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]
1.530.320.17-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.223
r_dihedral_angle_4_deg19.699
r_dihedral_angle_3_deg16.802
r_dihedral_angle_1_deg6.688
r_scangle_it6.637
r_scbond_it4.986
r_mcangle_it3.268
r_mcbond_it2.283
r_angle_refined_deg1.754
r_chiral_restr0.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.223
r_dihedral_angle_4_deg19.699
r_dihedral_angle_3_deg16.802
r_dihedral_angle_1_deg6.688
r_scangle_it6.637
r_scbond_it4.986
r_mcangle_it3.268
r_mcbond_it2.283
r_angle_refined_deg1.754
r_chiral_restr0.382
r_nbtor_refined0.31
r_nbd_refined0.213
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.11
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2311
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing