3GC8

The structure of p38beta C162S in complex with a dihydroquinazolinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GC7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429112% PEG 3350, 0.12 M ammonium fluoride, 30 uM CTAB, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.124α = 90
b = 157.71β = 91.57
c = 60.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102002-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00APS17-ID

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
12.43099.20.0888.94.92887328642-345.7
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)
12.42.5940.3361.25.42885

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3GC72.4302709527046144099.80.211710.208420.27192RANDOM34.968
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]
-0.430.04-0.741.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.264
r_dihedral_angle_3_deg17.184
r_dihedral_angle_4_deg16.593
r_dihedral_angle_1_deg5.892
r_scangle_it2.642
r_scbond_it1.665
r_angle_refined_deg1.389
r_mcangle_it1.205
r_mcbond_it0.652
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.264
r_dihedral_angle_3_deg17.184
r_dihedral_angle_4_deg16.593
r_dihedral_angle_1_deg5.892
r_scangle_it2.642
r_scbond_it1.665
r_angle_refined_deg1.389
r_mcangle_it1.205
r_mcbond_it0.652
r_nbtor_refined0.301
r_symmetry_vdw_refined0.293
r_nbd_refined0.21
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.146
r_symmetry_metal_ion_refined0.098
r_chiral_restr0.089
r_metal_ion_refined0.057
r_bond_refined_d0.012
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 Atoms5485
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms75

Software

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