3NNU

Crystal structure of P38 alpha in complex with DP1376


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729020% PEG 3350, 200MM LITIUM CITRATE, SOAKED WITH COMPOUND, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.0559.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.5α = 90
b = 86.183β = 90
c = 126.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9531.583.90.0760.0767.85.22492224922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.15771.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2.42017338173389130.180.180.1770.227RANDOM32.89
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]
0.03-0.840.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.724
r_dihedral_angle_4_deg19.422
r_dihedral_angle_3_deg16.696
r_dihedral_angle_1_deg6.347
r_scangle_it3.319
r_scbond_it2.068
r_mcangle_it1.63
r_angle_refined_deg1.591
r_mcbond_it0.922
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.724
r_dihedral_angle_4_deg19.422
r_dihedral_angle_3_deg16.696
r_dihedral_angle_1_deg6.347
r_scangle_it3.319
r_scbond_it2.068
r_mcangle_it1.63
r_angle_refined_deg1.591
r_mcbond_it0.922
r_nbtor_refined0.307
r_symmetry_vdw_refined0.252
r_nbd_refined0.208
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.124
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2804
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms32

Software

Software
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling