3G58 | pdb_00003g58

Crystal structure of human phosphodiesterase 4d with d155988/pmnpq


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
2.5752.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.385α = 90
b = 113.57β = 90
c = 161.129γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.055090.10.05813.35.8102588
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)
2.052.1253.10.4364.8

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 REPLACEMENTTHROUGHOUT2.0549.2110252951580.1730.1710.170.2130.21RANDOM22.54
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]
0.11-0.08-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.271
r_dihedral_angle_4_deg15.274
r_dihedral_angle_3_deg14.307
r_dihedral_angle_1_deg5.101
r_scangle_it3.042
r_scbond_it1.871
r_angle_refined_deg1.15
r_mcangle_it1.134
r_angle_other_deg0.887
r_mcbond_it0.584
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.271
r_dihedral_angle_4_deg15.274
r_dihedral_angle_3_deg14.307
r_dihedral_angle_1_deg5.101
r_scangle_it3.042
r_scbond_it1.871
r_angle_refined_deg1.15
r_mcangle_it1.134
r_angle_other_deg0.887
r_mcbond_it0.584
r_mcbond_other0.131
r_chiral_restr0.065
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10762
Nucleic Acid Atoms
Solvent Atoms1144
Heterogen Atoms185

Software

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