X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 279.0
Details 15.2 % PEG4000, 0.3 M lithium-sulfate, 0.1 M sodium-acetate pH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.01 α = 90
b = 71.01 β = 90
c = 234.85 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2013-02-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 0.97916 MAX II I911-3

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
1.9 29.43 100.0 -- 0.072 8.04 8.1 -- 48600 -- -- 18.22
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)
1.9 2.0 100.0 0.316 -- 2.2 8.2 --

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 1.9 29.429 -- 0.0 -- 48489 2452 99.95 -- 0.1571 0.1551 0.1949 Random selection
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 1.9 1.9366 -- 153 2518 0.1809 0.2418 -- 100.0
X Ray Diffraction 1.9366 1.9761 -- 130 2484 0.1749 0.2563 -- 100.0
X Ray Diffraction 1.9761 2.019 -- 144 2496 0.1565 0.2111 -- 100.0
X Ray Diffraction 2.019 2.066 -- 135 2505 0.1524 0.2134 -- 100.0
X Ray Diffraction 2.066 2.1176 -- 133 2521 0.1524 0.205 -- 100.0
X Ray Diffraction 2.1176 2.1749 -- 136 2510 0.1552 0.1819 -- 100.0
X Ray Diffraction 2.1749 2.2389 -- 136 2522 0.1567 0.2113 -- 100.0
X Ray Diffraction 2.2389 2.3111 -- 130 2516 0.1547 0.2146 -- 100.0
X Ray Diffraction 2.3111 2.3937 -- 136 2540 0.1564 0.2064 -- 100.0
X Ray Diffraction 2.3937 2.4894 -- 122 2531 0.1647 0.2322 -- 100.0
X Ray Diffraction 2.4894 2.6027 -- 124 2568 0.1642 0.2374 -- 100.0
X Ray Diffraction 2.6027 2.7398 -- 132 2562 0.1648 0.2051 -- 100.0
X Ray Diffraction 2.7398 2.9113 -- 156 2518 0.1682 0.2388 -- 100.0
X Ray Diffraction 2.9113 3.1359 -- 141 2573 0.169 0.204 -- 100.0
X Ray Diffraction 3.1359 3.451 -- 123 2604 0.1549 0.1917 -- 100.0
X Ray Diffraction 3.451 3.9494 -- 154 2600 0.1413 0.1667 -- 100.0
X Ray Diffraction 3.9494 4.9719 -- 138 2647 0.1252 0.1406 -- 100.0
X Ray Diffraction 4.9719 29.4321 -- 129 2822 0.1639 0.1694 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.11
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.053
f_plane_restr 0.005
f_bond_d 0.006
f_chiral_restr 0.075
f_dihedral_angle_d 13.799
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4042
Nucleic Acid Atoms 0
Heterogen Atoms 91
Solvent Atoms 582

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.8.2
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
XSCALE data scaling
XSCALE data reduction