X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 298.0
Details Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 10% glycerol, 50 mM MgCl2, 5 mM EDTA, 2 mM NiCl2; Reservoir (0.1 M HEPES:NaOH pH 7.5 70% (v/v) MPD); Soak 2 minutes in (Reservoir + 50 mM MgCl2, 200 mM 4-OH Proline Betaine ) Cryoprotection (Soaking solution), sitting drop vapor diffuction, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.04 α = 90
b = 152.82 β = 105.2
c = 113.03 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2012-04-14
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID -- APS 31-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
1.7 109.07 99.9 -- 0.085 -- 3.8 -- 325934 -- 0.0 --
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)
1.7 1.79 99.9 0.577 0.577 1.3 3.6 --

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 1.7 25.68 -- 0.0 325787 325787 16434 99.9 -- 0.16 0.159 0.192 --
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 1.7 1.7193 -- 522 10371 0.2359 0.2683 -- 100.0
X Ray Diffraction 1.7193 1.7395 -- 568 10272 0.2362 0.269 -- 100.0
X Ray Diffraction 1.7395 1.7607 -- 535 10326 0.2263 0.2591 -- 100.0
X Ray Diffraction 1.7607 1.783 -- 559 10190 0.2272 0.2583 -- 100.0
X Ray Diffraction 1.783 1.8065 -- 573 10257 0.221 0.2581 -- 100.0
X Ray Diffraction 1.8065 1.8312 -- 558 10341 0.2059 0.2387 -- 100.0
X Ray Diffraction 1.8312 1.8574 -- 562 10284 0.1958 0.2394 -- 100.0
X Ray Diffraction 1.8574 1.8851 -- 541 10284 0.1848 0.2186 -- 100.0
X Ray Diffraction 1.8851 1.9145 -- 540 10309 0.1737 0.2103 -- 100.0
X Ray Diffraction 1.9145 1.9459 -- 555 10285 0.1785 0.2186 -- 100.0
X Ray Diffraction 1.9459 1.9795 -- 528 10380 0.1758 0.2218 -- 100.0
X Ray Diffraction 1.9795 2.0154 -- 564 10250 0.1691 0.2127 -- 100.0
X Ray Diffraction 2.0154 2.0542 -- 532 10289 0.1608 0.2054 -- 100.0
X Ray Diffraction 2.0542 2.0961 -- 529 10303 0.1502 0.1886 -- 100.0
X Ray Diffraction 2.0961 2.1417 -- 511 10363 0.154 0.1995 -- 100.0
X Ray Diffraction 2.1417 2.1915 -- 546 10272 0.153 0.195 -- 100.0
X Ray Diffraction 2.1915 2.2462 -- 569 10313 0.1565 0.1983 -- 100.0
X Ray Diffraction 2.2462 2.3069 -- 544 10304 0.1488 0.193 -- 100.0
X Ray Diffraction 2.3069 2.3748 -- 526 10359 0.1527 0.1867 -- 100.0
X Ray Diffraction 2.3748 2.4514 -- 530 10325 0.1568 0.1887 -- 100.0
X Ray Diffraction 2.4514 2.5389 -- 545 10338 0.159 0.1934 -- 100.0
X Ray Diffraction 2.5389 2.6404 -- 582 10264 0.1551 0.1904 -- 100.0
X Ray Diffraction 2.6404 2.7605 -- 539 10372 0.165 0.1961 -- 100.0
X Ray Diffraction 2.7605 2.9058 -- 563 10300 0.1603 0.191 -- 100.0
X Ray Diffraction 2.9058 3.0876 -- 562 10309 0.1576 0.2033 -- 100.0
X Ray Diffraction 3.0876 3.3256 -- 578 10310 0.1423 0.1648 -- 100.0
X Ray Diffraction 3.3256 3.6594 -- 528 10393 0.1378 0.1707 -- 100.0
X Ray Diffraction 3.6594 4.1869 -- 535 10373 0.1257 0.1476 -- 100.0
X Ray Diffraction 4.1869 5.2676 -- 521 10408 0.1347 0.1616 -- 100.0
X Ray Diffraction 5.2676 25.6847 -- 589 10209 0.1737 0.1974 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.53
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.074
f_dihedral_angle_d 12.802
f_angle_d 1.109
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22160
Nucleic Acid Atoms 0
Heterogen Atoms 183
Solvent Atoms 2066

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.16 data reduction