3HL7

Crystal Structure of Human p38alpha complexed with SD-0006


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929820-30% PEG3000, 10 mM CaCl2, 50 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.088α = 90
b = 74.525β = 90
c = 77.587γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mm2002-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BM1.0APS17-BM

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
11.88401000.0540.05434.66.53071530175-1.5-328.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9777.50.4540.4542.54.52405

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT1.8824.8429122154798.420.200060.198580.22825RANDOM29.233
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]
0.01-1.191.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg16.765
r_dihedral_angle_3_deg16.684
r_dihedral_angle_1_deg5.339
r_scangle_it2.522
r_scbond_it1.66
r_angle_refined_deg1.285
r_mcangle_it1.229
r_angle_other_deg0.898
r_mcbond_it0.731
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg16.765
r_dihedral_angle_3_deg16.684
r_dihedral_angle_1_deg5.339
r_scangle_it2.522
r_scbond_it1.66
r_angle_refined_deg1.285
r_mcangle_it1.229
r_angle_other_deg0.898
r_mcbond_it0.731
r_nbd_refined0.208
r_symmetry_vdw_other0.208
r_nbd_other0.188
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.17
r_mcbond_other0.135
r_symmetry_hbond_refined0.129
r_symmetry_vdw_refined0.109
r_nbtor_other0.089
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2698
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms47

Software

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