X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details 0.16 M MgCl2, 0.08 M Tris-HCl, 24% (w/v) PEG 4000, 20% (v/v) glycerol and directly frozen for data collection , VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.4 α = 78.11
b = 59.25 β = 78.09
c = 97.46 γ = 78.85
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2

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
2.75 46.96 96.1 0.069 -- -- 1.91 -- 31399 2.0 1.5 --
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)
2.75 2.85 95.6 0.468 -- 1.8 1.91 3149

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 2.75 46.959 -- 1.96 -- 31380 1602 96.04 -- 0.2047 0.2016 0.2623 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 2.75 2.8388 -- 132 2735 0.3026 0.3137 -- 95.0
X Ray Diffraction 2.8388 2.9402 -- 169 2671 0.288 0.3545 -- 96.0
X Ray Diffraction 2.9402 3.0579 -- 142 2684 0.2806 0.3358 -- 96.0
X Ray Diffraction 3.0579 3.1971 -- 142 2717 0.2625 0.3541 -- 96.0
X Ray Diffraction 3.1971 3.3656 -- 162 2697 0.2721 0.3534 -- 96.0
X Ray Diffraction 3.3656 3.5764 -- 139 2727 0.2284 0.2723 -- 97.0
X Ray Diffraction 3.5764 3.8524 -- 152 2694 0.204 0.3121 -- 96.0
X Ray Diffraction 3.8524 4.2398 -- 142 2745 0.1753 0.2311 -- 96.0
X Ray Diffraction 4.2398 4.8528 -- 129 2712 0.1588 0.2107 -- 96.0
X Ray Diffraction 4.8528 6.1119 -- 147 2699 0.1832 0.2281 -- 96.0
X Ray Diffraction 6.1119 46.9656 -- 146 2697 0.1792 0.2294 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.9464
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.6
f_plane_restr 0.007
f_chiral_restr 0.052
f_angle_d 1.216
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7402
Nucleic Acid Atoms 1418
Heterogen Atoms 26
Solvent Atoms 98

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
d*TREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.9.1L data reduction