3FMN

P38 kinase crystal structure in complex with RO2530


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
2.957.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.866α = 90
b = 86.559β = 90
c = 124.781γ = 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
11.95098.80.0474.63953529.4
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)
11.91.9794.90.4962.13.63731

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 1P381.943.2737306197198.170.20570.203760.24188RANDOM30.923
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]
-0.67-0.30.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg16.742
r_dihedral_angle_3_deg11.346
r_dihedral_angle_1_deg4.645
r_scangle_it1.757
r_angle_refined_deg1.114
r_scbond_it1.052
r_mcangle_it0.968
r_mcbond_it0.542
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg16.742
r_dihedral_angle_3_deg11.346
r_dihedral_angle_1_deg4.645
r_scangle_it1.757
r_angle_refined_deg1.114
r_scbond_it1.052
r_mcangle_it0.968
r_mcbond_it0.542
r_nbtor_refined0.299
r_nbd_refined0.192
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.11
r_symmetry_hbond_refined0.08
r_chiral_restr0.062
r_bond_refined_d0.007
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 Atoms2756
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing