X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 1.2M tri-sodium citrate, 100mM Hepes, 3.5% 1,2-propanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.41 α = 90
b = 61.75 β = 102.91
c = 118.66 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1

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
2.35 115.66 97.2 0.046 0.046 -- 2.8 26894 26894 -- -- --
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)
2.35 2.48 88.9 0.169 0.169 3.4 2.4 3557

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 2.35 33.32 -- 0.01 -- 26301 1316 95.03 -- 0.2042 0.2008 0.2692 --
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 2.35 2.4441 -- 127 2278 0.2118 0.2968 -- 79.0
X Ray Diffraction 2.4441 2.5553 -- 143 2731 0.2192 0.2913 -- 94.0
X Ray Diffraction 2.5553 2.6899 -- 140 2802 0.2164 0.3278 -- 96.0
X Ray Diffraction 2.6899 2.8584 -- 139 2822 0.2108 0.2998 -- 98.0
X Ray Diffraction 2.8584 3.0789 -- 160 2870 0.2061 0.3235 -- 99.0
X Ray Diffraction 3.0789 3.3885 -- 151 2890 0.2052 0.2867 -- 99.0
X Ray Diffraction 3.3885 3.8782 -- 138 2929 0.1743 0.2459 -- 100.0
X Ray Diffraction 3.8782 4.8837 -- 153 2931 0.1509 0.2092 -- 100.0
X Ray Diffraction 4.8837 33.3234 -- 165 2732 0.1903 0.2311 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.2753
Anisotropic B[1][1] 6.6926
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.3844
Anisotropic B[2][2] 10.0061
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.6987
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.058
f_chiral_restr 0.067
f_dihedral_angle_d 17.751
f_plane_restr 0.004
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4039
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 231

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.19
PHENIX refinement version: 1.6_289
PDB_EXTRACT data extraction version: 3.10
DNA data collection
MOSFLM data reduction
REFMAC phasing