X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.2
Temperature 298.0
Details 28-30% PEG 6000, 0.1 M Tris, pH 8.2, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.26 α = 90
b = 73.09 β = 91.45
c = 80.93 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 MARMOSAIC 300 mm CCD -- 2008-04-12
Diffraction Radiation
Monochromator Protocol
Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.92309 APS 22-ID

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
2.15 50 99.0 0.076 -- -- 5.2 43654 43654 0.0 0.0 40.4
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)
2.15 2.19 91.8 0.615 -- -- 4.6 2026

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 2.15 25.348 -- 1.34 43654 43619 2200 98.76 -- 0.195 0.1921 0.2493 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 2.15 2.1951 -- 124 2313 0.2588 0.333 -- 89.0
X Ray Diffraction 2.1951 2.2461 -- 132 2541 0.263 0.3294 -- 97.0
X Ray Diffraction 2.2461 2.3023 -- 137 2554 0.2646 0.3628 -- 99.0
X Ray Diffraction 2.3023 2.3645 -- 128 2601 0.258 0.3439 -- 100.0
X Ray Diffraction 2.3645 2.434 -- 128 2598 0.2496 0.3253 -- 100.0
X Ray Diffraction 2.434 2.5125 -- 167 2585 0.2575 0.324 -- 100.0
X Ray Diffraction 2.5125 2.6022 -- 132 2594 0.2422 0.3695 -- 99.0
X Ray Diffraction 2.6022 2.7063 -- 126 2613 0.2387 0.2935 -- 100.0
X Ray Diffraction 2.7063 2.8293 -- 138 2593 0.2205 0.3043 -- 100.0
X Ray Diffraction 2.8293 2.9782 -- 159 2584 0.2258 0.2984 -- 100.0
X Ray Diffraction 2.9782 3.1645 -- 132 2640 0.2131 0.306 -- 100.0
X Ray Diffraction 3.1645 3.4083 -- 120 2630 0.2072 0.2883 -- 100.0
X Ray Diffraction 3.4083 3.7503 -- 158 2600 0.1928 0.2539 -- 100.0
X Ray Diffraction 3.7503 4.2907 -- 137 2637 0.164 0.1916 -- 100.0
X Ray Diffraction 4.2907 5.3973 -- 130 2664 0.1346 0.1844 -- 100.0
X Ray Diffraction 5.3973 25.3498 -- 152 2672 0.1605 0.1862 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.0103
Anisotropic B[1][1] -8.2967
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.3411
Anisotropic B[2][2] -4.573
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.8696
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.845
f_plane_restr 0.003
f_chiral_restr 0.073
f_angle_d 0.903
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6183
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 176

Software

Computing
Computing Package Purpose
In house software Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
CCP4-FFT Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction