X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 277.0
Details 100 mM sodium formate, 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.28 α = 90
b = 114.58 β = 90
c = 124.66 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 MARMOSAIC 300 mm CCD -- 2013-02-02
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-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
2.54 50 99.3 0.079 -- -- 4.0 19773 19635 1.0 1.0 61.87
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)
2.541 2.64 100.0 0.582 -- -- 4.1 1921

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 2.541 39.063 -- 1.37 19773 19503 1002 98.62 -- 0.211 0.2084 0.2599 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 2.541 2.6745 -- 118 2581 0.3442 0.4316 -- 98.0
X Ray Diffraction 2.6745 2.8421 -- 157 2594 0.314 0.3337 -- 100.0
X Ray Diffraction 2.8421 3.0614 -- 150 2622 0.2882 0.3541 -- 100.0
X Ray Diffraction 3.0614 3.3693 -- 129 2645 0.2184 0.2726 -- 98.0
X Ray Diffraction 3.3693 3.8565 -- 142 2620 0.2155 0.2837 -- 99.0
X Ray Diffraction 3.8565 4.8574 -- 147 2695 0.1784 0.2294 -- 99.0
X Ray Diffraction 4.8574 39.0679 -- 159 2744 0.1717 0.2141 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 88.5488
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.484
f_plane_restr 0.007
f_chiral_restr 0.048
f_angle_d 1.223
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2921
Nucleic Acid Atoms 818
Heterogen Atoms 46
Solvent Atoms 25

Software

Computing
Computing Package Purpose
SER-gui Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.2_1309) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection