1TB5

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With AMP


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 10
Temperature 277.0
Details ammonium sulfate, lithium sulfate, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.55 α = 90
b = 94.24 β = 90
c = 107.24 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2003-08-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.15 70.71 -- 0.079 -- -- 4.7 46988 46988 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.15 2.206 100.0 0.751 -- 1.63 4.7 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.15 70.71 -- -- 46988 46988 2505 98.91 -- 0.23544 0.23362 0.26822 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.15 2.206 -- 164 3361 0.347 0.404 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 29.352
Anisotropic B[1][1] -3.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.75
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.178
r_symmetry_hbond_refined 0.177
r_metal_ion_refined 0.121
r_bond_refined_d 0.015
r_angle_refined_deg 1.502
r_symmetry_vdw_refined 0.143
r_bond_other_d 0.002
r_nbd_other 0.222
r_chiral_restr 0.096
r_nbd_refined 0.221
r_symmetry_vdw_other 0.313
r_scbond_it 1.974
r_gen_planes_other 0.008
r_mcbond_it 0.606
r_gen_planes_refined 0.009
r_nbtor_other 0.093
r_scangle_it 3.092
r_mcangle_it 1.113
r_angle_other_deg 0.937
r_dihedral_angle_1_deg 3.214
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.235
Luzzati ESD (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5226
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 69

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.25
Blu-Ice data collection
ELVES data scaling
EPMR phasing