3G4I

Crystal structure of human phosphodiesterase 4d with d155871


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5852.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.865α = 90
b = 113.241β = 90
c = 161.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97ALS5.0.1

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
11.95092.90.0578.93.8132652
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)
1.91.9793.30.5812.9

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.95013246665960.1830.1810.215RANDOM20.39
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]
0.73-0.860.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.127
r_dihedral_angle_4_deg16.616
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg4.984
r_scangle_it2.609
r_scbond_it1.786
r_angle_refined_deg1.157
r_mcangle_it1.093
r_angle_other_deg0.945
r_mcbond_it0.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.127
r_dihedral_angle_4_deg16.616
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg4.984
r_scangle_it2.609
r_scbond_it1.786
r_angle_refined_deg1.157
r_mcangle_it1.093
r_angle_other_deg0.945
r_mcbond_it0.789
r_symmetry_vdw_other0.253
r_symmetry_vdw_refined0.231
r_nbd_refined0.215
r_xyhbond_nbd_refined0.195
r_symmetry_hbond_refined0.188
r_nbd_other0.183
r_nbtor_refined0.17
r_mcbond_other0.155
r_nbtor_other0.083
r_chiral_restr0.066
r_metal_ion_refined0.015
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10655
Nucleic Acid Atoms
Solvent Atoms1203
Heterogen Atoms159

Software

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