3FMM

P38 kinase crystal structure in complex with RO6226


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.629050 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.9157.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.802α = 90
b = 87.369β = 90
c = 124.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0000ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125098.50.0594.23422836.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0797.80.4512.73.53336

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1P38233.9832383171798.570.214350.21290.24151RANDOM37.7
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]
-0.72-0.391.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_dihedral_angle_4_deg17.983
r_dihedral_angle_3_deg12.313
r_dihedral_angle_1_deg4.933
r_scangle_it1.902
r_scbond_it1.146
r_angle_refined_deg1.071
r_mcangle_it1.017
r_mcbond_it0.58
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_dihedral_angle_4_deg17.983
r_dihedral_angle_3_deg12.313
r_dihedral_angle_1_deg4.933
r_scangle_it1.902
r_scbond_it1.146
r_angle_refined_deg1.071
r_mcangle_it1.017
r_mcbond_it0.58
r_nbtor_refined0.299
r_nbd_refined0.187
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.112
r_symmetry_hbond_refined0.081
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms2791
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing