X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 293.0
Details 1.1M Sodium citrate, 0.1M MES PH 7.1, 5mg/ml protein, incubated overnight at 4deg with final concentration of 0.5mM gefitinib and 1% DMSO , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 143.68 α = 90
b = 143.68 β = 90
c = 143.68 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-10-17
Diffraction Radiation
Monochromator Protocol
FIXED EXIT SI DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2

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
2.5 45.45 100.0 -- 0.093 -- 45.3 -- 17240 -- -3.0 51.72
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)
2.5 2.64 100.0 0.449 0.45 1.7 45.7 2503

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 2.5 45.45 -- 0.0 -- 17208 868 100.0 0.19 -- 0.186 0.249 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 2.5 2.57 1179 67 1179 0.27 0.38 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.47
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.179
r_scangle_it 5.926
r_dihedral_angle_1_deg 6.81
r_mcangle_it 2.456
r_angle_refined_deg 2.202
r_symmetry_vdw_refined 0.227
r_bond_refined_d 0.025
r_dihedral_angle_2_deg 40.655
r_nbd_refined 0.238
r_dihedral_angle_3_deg 19.233
r_dihedral_angle_4_deg 20.719
r_mcbond_it 1.792
r_symmetry_hbond_refined 0.261
r_gen_planes_refined 0.009
r_chiral_restr 0.127
r_nbtor_refined 0.334
r_scbond_it 4.374
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2338
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 55

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
MOSFLM data reduction
SCALA data scaling