X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.77
Temperature 295.0
Details 100 mM sodium citrate, 1.5 M ammonium sulfate, pH 4.77, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.03 α = 90
b = 106.03 β = 90
c = 221.55 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2013-11-20
Diffraction Radiation
Monochromator Protocol
double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.979390 APS 23-ID-D

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 91.82 -- -- 0.13 -- 3.7 57289 57046 -- -- --
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 2.47 99.4 -- 0.73 1.7 3.7 4388

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 47.819 -- 1.36 -- 57040 2888 99.6 -- 0.2161 0.2144 0.2473 --
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 2.399 2.4385 -- 119 2481 0.2927 0.3225 -- 97.0
X Ray Diffraction 2.4385 2.4805 -- 140 2585 0.2742 0.3235 -- 100.0
X Ray Diffraction 2.4805 2.5256 -- 147 2534 0.2699 0.2997 -- 100.0
X Ray Diffraction 2.5256 2.5742 -- 142 2519 0.2567 0.3283 -- 100.0
X Ray Diffraction 2.5742 2.6267 -- 124 2559 0.2625 0.2997 -- 100.0
X Ray Diffraction 2.6267 2.6839 -- 152 2538 0.2768 0.343 -- 100.0
X Ray Diffraction 2.6839 2.7463 -- 143 2565 0.2628 0.2535 -- 100.0
X Ray Diffraction 2.7463 2.815 -- 120 2583 0.264 0.3639 -- 100.0
X Ray Diffraction 2.815 2.8911 -- 157 2521 0.2671 0.2959 -- 100.0
X Ray Diffraction 2.8911 2.9761 -- 132 2548 0.2699 0.3127 -- 100.0
X Ray Diffraction 2.9761 3.0722 -- 127 2595 0.2672 0.2873 -- 100.0
X Ray Diffraction 3.0722 3.1819 -- 142 2554 0.251 0.2958 -- 100.0
X Ray Diffraction 3.1819 3.3093 -- 139 2602 0.2497 0.2821 -- 100.0
X Ray Diffraction 3.3093 3.4599 -- 138 2573 0.2233 0.2558 -- 100.0
X Ray Diffraction 3.4599 3.6422 -- 131 2602 0.1981 0.2504 -- 100.0
X Ray Diffraction 3.6422 3.8703 -- 137 2554 0.1647 0.1847 -- 100.0
X Ray Diffraction 3.8703 4.169 -- 138 2628 0.1573 0.1902 -- 100.0
X Ray Diffraction 4.169 4.5882 -- 135 2605 0.1623 0.1889 -- 100.0
X Ray Diffraction 4.5882 5.2515 -- 153 2621 0.1629 0.2135 -- 100.0
X Ray Diffraction 5.2515 6.6135 -- 143 2650 0.2066 0.2204 -- 99.0
X Ray Diffraction 6.6135 47.8283 -- 129 2735 0.2134 0.2265 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_dihedral_angle_d 15.907
f_angle_d 1.501
f_bond_d 0.009
f_chiral_restr 0.101
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6232
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 120

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
XDS data reduction
XDS data scaling