X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 289.0
Details 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. Crystals soaked with 6.7mM inhibitor in 20% DMSO for 3 hrs, SMALL TUBES, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.27 α = 90
b = 128.27 β = 90
c = 115.78 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-11-19
Diffraction Radiation
Monochromator Protocol
Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 1.04498 SRS PX10.1

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
2.05 35.7 99.7 0.093 -- -- 6.4 60721 60721 0.0 -3.0 --
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)
2.05 2.16 100.0 0.45 -- 5.6 6.3 --

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
FOURIER SYNTHESIS 2.05 35.69 -- -- 57608 57607 3081 99.51 -- 0.17503 0.17344 0.20498 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 2.05 2.103 -- 221 4240 0.215 0.267 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.436
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.082
r_nbtor_refined 0.305
r_symmetry_hbond_refined 0.122
r_nbd_refined 0.183
r_dihedral_angle_4_deg 20.823
r_bond_refined_d 0.009
r_mcbond_it 0.628
r_symmetry_vdw_refined 0.151
r_dihedral_angle_1_deg 5.424
r_scangle_it 3.154
r_dihedral_angle_3_deg 15.713
r_angle_refined_deg 1.147
r_xyhbond_nbd_refined 0.097
r_scbond_it 1.838
r_dihedral_angle_2_deg 33.749
r_gen_planes_refined 0.004
r_mcangle_it 1.224
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6604
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 299

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CNS refinement
HKL-3000 data collection
DENZO data reduction
SCALEPACK data scaling
CNS phasing