X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 293.0
Details 14% PEG 3350, 125 mM sodium malonate, 1 mM TCEP and 0.1 M Bis-Tris propane pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.87 α = 90
b = 84.62 β = 90
c = 101.14 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2009-05-07
Diffraction Radiation
Monochromator Protocol
RH COATED SI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 -- CHESS A1

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 45 95.6 0.077 -- -- 3.8 -- 16073 -- -- --
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 2.43 97.8 0.244 -- -- 4.1 --

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 39.64 -- 1.34 -- 15916 807 95.6 -- 0.212 0.21 0.253 --
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 2.4972 -- 142 2508 0.2668 0.3314 -- 97.0
X Ray Diffraction 2.4972 2.69 -- 138 2516 0.2483 0.3312 -- 98.0
X Ray Diffraction 2.69 2.9606 -- 153 2512 0.2361 0.3062 -- 97.0
X Ray Diffraction 2.9606 3.3888 -- 135 2525 0.2102 0.269 -- 96.0
X Ray Diffraction 3.3888 4.2688 -- 125 2499 0.1844 0.2102 -- 94.0
X Ray Diffraction 4.2688 39.6449 -- 114 2549 0.1971 0.2071 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.91
Anisotropic B[1][1] 10.6732
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.4121
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.2611
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.093
f_dihedral_angle_d 16.277
f_angle_d 1.283
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2308
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 96

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
AUTOMR Structure Solution
PHENIX (PHENIX.REFINE: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data reduction