X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 306.0
Details 2.6 M sodium acetate, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 306K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.95 α = 90
b = 117.56 β = 90
c = 160.38 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 315r -- 2012-11-15
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97 SSRF BL17U

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
2.49 50 99.9 0.127 -- -- 6.6 -- 73777 2.07 2.0 46.62
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)
2.489 2.59 99.5 0.92 -- -- 6.0 7255

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 2.489 48.161 -- 1.35 73688 73688 3714 99.42 -- 0.2026 0.2003 0.2452 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 2.489 2.5208 -- 126 2251 0.3407 0.4025 -- 87.0
X Ray Diffraction 2.5208 2.5539 -- 144 2546 0.3043 0.2957 -- 100.0
X Ray Diffraction 2.5539 2.5889 -- 131 2584 0.2827 0.3331 -- 100.0
X Ray Diffraction 2.5889 2.6259 -- 130 2560 0.2775 0.3132 -- 100.0
X Ray Diffraction 2.6259 2.6651 -- 127 2570 0.302 0.3567 -- 100.0
X Ray Diffraction 2.6651 2.7067 -- 135 2575 0.2882 0.3793 -- 100.0
X Ray Diffraction 2.7067 2.7511 -- 134 2582 0.2503 0.3141 -- 100.0
X Ray Diffraction 2.7511 2.7985 -- 145 2574 0.2451 0.2893 -- 100.0
X Ray Diffraction 2.7985 2.8494 -- 128 2604 0.2355 0.2969 -- 100.0
X Ray Diffraction 2.8494 2.9042 -- 131 2557 0.233 0.282 -- 100.0
X Ray Diffraction 2.9042 2.9635 -- 140 2607 0.2271 0.2843 -- 100.0
X Ray Diffraction 2.9635 3.0279 -- 146 2564 0.2318 0.2727 -- 100.0
X Ray Diffraction 3.0279 3.0983 -- 117 2635 0.2141 0.2981 -- 100.0
X Ray Diffraction 3.0983 3.1758 -- 137 2585 0.2017 0.2926 -- 100.0
X Ray Diffraction 3.1758 3.2617 -- 137 2593 0.1959 0.2503 -- 100.0
X Ray Diffraction 3.2617 3.3576 -- 142 2600 0.1889 0.2257 -- 100.0
X Ray Diffraction 3.3576 3.466 -- 143 2573 0.2121 0.2643 -- 100.0
X Ray Diffraction 3.466 3.5898 -- 134 2598 0.1895 0.2434 -- 100.0
X Ray Diffraction 3.5898 3.7335 -- 143 2587 0.2125 0.2478 -- 100.0
X Ray Diffraction 3.7335 3.9033 -- 145 2595 0.1994 0.2344 -- 100.0
X Ray Diffraction 3.9033 4.109 -- 164 2579 0.1733 0.2192 -- 100.0
X Ray Diffraction 4.109 4.3663 -- 158 2612 0.1567 0.1946 -- 100.0
X Ray Diffraction 4.3663 4.7032 -- 141 2610 0.1513 0.2041 -- 100.0
X Ray Diffraction 4.7032 5.176 -- 146 2653 0.1663 0.2154 -- 100.0
X Ray Diffraction 5.176 5.9238 -- 134 2659 0.1917 0.2514 -- 100.0
X Ray Diffraction 5.9238 7.4589 -- 128 2706 0.1991 0.219 -- 100.0
X Ray Diffraction 7.4589 48.1698 -- 128 2815 0.1745 0.189 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.9704
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.034
f_dihedral_angle_d 17.289
f_bond_d 0.01
f_plane_restr 0.004
f_angle_d 0.906
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10627
Nucleic Acid Atoms 1311
Heterogen Atoms 48
Solvent Atoms 320

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection