4ASX

Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q4TPDB ENTRY 3Q4T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120 % PEG 3350 0.20 M NA(MALONATE)
Crystal Properties
Matthews coefficientSolvent content
2.6253.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.426α = 90
b = 110.426β = 90
c = 208.848γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.0519.9999.70.1384.547777225.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1699.80.821.94.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3Q4T2.0519.9945307241499.580.188440.186520.2254RANDOM25.745
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]
0.310.150.31-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_4_deg20.123
r_dihedral_angle_3_deg14.179
r_dihedral_angle_1_deg6.188
r_mcangle_it2.912
r_mcbond_it1.774
r_angle_refined_deg1.552
r_angle_other_deg1.466
r_nbd_refined0.262
r_symmetry_vdw_other0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_4_deg20.123
r_dihedral_angle_3_deg14.179
r_dihedral_angle_1_deg6.188
r_mcangle_it2.912
r_mcbond_it1.774
r_angle_refined_deg1.552
r_angle_other_deg1.466
r_nbd_refined0.262
r_symmetry_vdw_other0.245
r_symmetry_vdw_refined0.228
r_nbd_other0.221
r_nbtor_refined0.185
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.145
r_nbtor_other0.115
r_xyhbond_nbd_other0.093
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.004
r_mcbond_other0.003
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4872
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing