6NJJ | pdb_00006njj

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32988.8MG/ML VCID7620 + 0.5MM BPN- 014770 (EBSI4045) IN A PROTEIN SOLUTION CONTAINING 10MM HEPES PH 7.5, 100MM NACL, 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214057) AGAINST OPTIMIZATION SCREEN TET_MPC8_JCH7 (OPT SCREEN BASED ON MORPHEUS C8 AND JCSG H7); 6.25% W/V PEG1,000, 20.91% W/V PEG3350, 6.25% W/V MPD, 0.2M AMMONIUM SULFATE, 0.1MM BIS- TRIS PH 6.3, CRYO-PROTECTED - 20% ETHYLENE GLYCOL, CRYSTAL TRACKING ID 247599D11 (WEV9-9), PH 6.30, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.33α = 90
b = 82.05β = 110.01
c = 116.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.35099.70.0860.99813.683.864038-339.87
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3699.80.5580.8592.63.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.345.4964022324199.80.170.1670.180.2140.22RANDOM31.06
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]
-0.05-2.451.590.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg15.934
r_dihedral_angle_3_deg13.576
r_dihedral_angle_1_deg5.154
r_mcangle_it3.847
r_mcbond_it2.627
r_mcbond_other2.627
r_angle_refined_deg1.578
r_angle_other_deg1.226
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg15.934
r_dihedral_angle_3_deg13.576
r_dihedral_angle_1_deg5.154
r_mcangle_it3.847
r_mcbond_it2.627
r_mcbond_other2.627
r_angle_refined_deg1.578
r_angle_other_deg1.226
r_chiral_restr0.09
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms10543
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling