X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 291.0
Details 0.2 M ammonium acetate, 0.1 M trisodium citrate, pH 5.5, 14% PEG400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.82 α = 90
b = 80.85 β = 90
c = 181.83 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 -- 2015-03-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-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
2.49 181.83 99.5 0.049 -- -- 4.7 -- 35240 -- -- 61.69
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)
2.488 2.51 -- 0.734 -- -- -- --

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 2.488 45.458 -- 1.34 -- 35149 1774 99.32 -- 0.2079 0.2054 0.2542 --
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 2.4881 2.5554 -- 125 2529 0.2712 0.3193 0.0 100.0
X Ray Diffraction 2.5554 2.6306 -- 160 2511 0.2679 0.3371 0.0 100.0
X Ray Diffraction 2.6306 2.7155 -- 141 2543 0.2703 0.344 0.0 100.0
X Ray Diffraction 2.7155 2.8125 -- 132 2528 0.2551 0.3274 0.0 100.0
X Ray Diffraction 2.8125 2.9251 -- 124 2598 0.2579 0.346 0.0 100.0
X Ray Diffraction 2.9251 3.0582 -- 122 2557 0.2493 0.2463 0.0 100.0
X Ray Diffraction 3.0582 3.2194 -- 121 2584 0.2456 0.3084 0.0 100.0
X Ray Diffraction 3.2194 3.421 -- 119 2567 0.2272 0.2841 0.0 100.0
X Ray Diffraction 3.421 3.685 -- 134 2588 0.2085 0.257 0.0 100.0
X Ray Diffraction 3.685 4.0557 -- 163 2566 0.1862 0.225 0.0 100.0
X Ray Diffraction 4.0557 4.642 -- 120 2606 0.1601 0.2221 0.0 100.0
X Ray Diffraction 4.642 5.8465 -- 169 2632 0.1809 0.2222 0.0 100.0
X Ray Diffraction 5.8465 45.4651 -- 144 2566 0.199 0.2443 0.0 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 78.5625
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.9
f_dihedral_angle_d 14.727
f_chiral_restr 0.049
f_plane_restr 0.005
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5337
Nucleic Acid Atoms 640
Heterogen Atoms 58
Solvent Atoms 50

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10_2155
SCALA data scaling
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing