X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 294.0
Details 100 mM Tris-HCl, 13-15% PEG 4000, 200 mM MgCl2, 6.25% PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.36 α = 90
b = 83.07 β = 109.33
c = 129.86 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
PIXEL DECTRIS PILATUS 6M-F -- 2014-07-30
Diffraction Radiation
Monochromator Protocol
Si 220 filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C

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
2.4 102.3 97.68 0.08799 -- -- 3.4 -- 83492 -- -- --
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)
2.399 2.485 93.22 -- -- 0.99 3.3 --

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 2.399 102.252 -- 1.89 -- 83480 4167 97.67 -- 0.1976 0.1957 0.2329 --
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 2.3991 2.4263 -- 117 2314 0.3837 0.4185 -- 86.0
X Ray Diffraction 2.4263 2.4549 -- 134 2602 0.3908 0.3917 -- 96.0
X Ray Diffraction 2.4549 2.4848 -- 132 2640 0.3719 0.3706 -- 97.0
X Ray Diffraction 2.4848 2.5163 -- 124 2648 0.3569 0.382 -- 98.0
X Ray Diffraction 2.5163 2.5494 -- 120 2552 0.3502 0.4079 -- 96.0
X Ray Diffraction 2.5494 2.5843 -- 136 2643 0.3268 0.3828 -- 98.0
X Ray Diffraction 2.5843 2.6212 -- 170 2647 0.3027 0.3313 -- 99.0
X Ray Diffraction 2.6212 2.6603 -- 136 2669 0.2849 0.3101 -- 99.0
X Ray Diffraction 2.6603 2.7019 -- 137 2692 0.2703 0.2802 -- 99.0
X Ray Diffraction 2.7019 2.7462 -- 123 2669 0.2684 0.3053 -- 99.0
X Ray Diffraction 2.7462 2.7936 -- 121 2706 0.266 0.2855 -- 99.0
X Ray Diffraction 2.7936 2.8444 -- 157 2667 0.2516 0.3086 -- 99.0
X Ray Diffraction 2.8444 2.8991 -- 141 2641 0.2501 0.2845 -- 99.0
X Ray Diffraction 2.8991 2.9583 -- 162 2659 0.2431 0.2815 -- 99.0
X Ray Diffraction 2.9583 3.0226 -- 137 2644 0.2453 0.2993 -- 98.0
X Ray Diffraction 3.0226 3.0929 -- 146 2645 0.2519 0.2912 -- 98.0
X Ray Diffraction 3.0929 3.1703 -- 144 2593 0.2476 0.261 -- 97.0
X Ray Diffraction 3.1703 3.256 -- 148 2657 0.2229 0.2301 -- 99.0
X Ray Diffraction 3.256 3.3518 -- 138 2684 0.2104 0.2713 -- 99.0
X Ray Diffraction 3.3518 3.46 -- 127 2701 0.1956 0.2674 -- 99.0
X Ray Diffraction 3.46 3.5837 -- 154 2642 0.1865 0.237 -- 99.0
X Ray Diffraction 3.5837 3.7272 -- 129 2692 0.178 0.2149 -- 98.0
X Ray Diffraction 3.7272 3.8968 -- 142 2640 0.1657 0.2075 -- 98.0
X Ray Diffraction 3.8968 4.1022 -- 144 2551 0.1555 0.2296 -- 95.0
X Ray Diffraction 4.1022 4.3593 -- 158 2674 0.14 0.1696 -- 98.0
X Ray Diffraction 4.3593 4.6959 -- 156 2658 0.1323 0.157 -- 98.0
X Ray Diffraction 4.6959 5.1684 -- 128 2708 0.134 0.1801 -- 98.0
X Ray Diffraction 5.1684 5.9162 -- 136 2686 0.1673 0.2131 -- 98.0
X Ray Diffraction 5.9162 7.4535 -- 133 2662 0.1686 0.2173 -- 97.0
X Ray Diffraction 7.4535 102.345 -- 137 2727 0.16 0.1706 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.0026
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.031
f_plane_restr 0.003
f_bond_d 0.004
f_angle_d 0.686
f_dihedral_angle_d 16.853
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11538
Nucleic Acid Atoms 1640
Heterogen Atoms 108
Solvent Atoms 403

Software

Software
Software Name Purpose
PHENIX refinement
XSCALE data scaling
Coot model building
PHASER phasing
XDS data reduction