3ODY

Crystal structure of p38alpha Y323Q active mutant


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 17% PEG 3350, 0.15 M KF, 0.1 M Hepes, 25mM b-OG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.9 α = 90
b = 71.82 β = 95.24
c = 63.54 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-06-15
Diffraction Radiation
Monochromator Protocol
optical hatch of beamline SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.93 ESRF ID29

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
2.2 50 98.2 -- -- -- 3.3 16913 16913 1.0 1.0 38.15
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)
2.2 2.24 95.7 -- -- -- -- --

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
molrep 2.2 33.801 -- 1.34 16913 15566 758 89.87 0.2385 0.226 0.2219 0.3044 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 2.2 2.3698 -- 141 2994 0.3019 0.3641 -- 91.0
X Ray Diffraction 2.3698 2.6082 -- 155 3060 0.2812 0.3989 -- 94.0
X Ray Diffraction 2.6082 2.9855 -- 168 3142 0.2579 0.3335 -- 96.0
X Ray Diffraction 2.9855 3.7606 -- 165 2907 0.2097 0.3335 -- 88.0
X Ray Diffraction 3.7606 33.8051 -- 129 2705 0.1869 0.2448 -- 81.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.012
f_chiral_restr 0.086
f_plane_restr 0.006
f_angle_d 1.434
f_dihedral_angle_d 19.567
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2604
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 12

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
PHENIX refinement version: (phenix.refine: dev_392)
HKL-2000 data reduction
HKL-2000 data scaling