X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details VAPOUR DIFFUSION (1:1 MIX): 17 % PEG 3350, 0.02 M NAK PHOSPHATE AND 0.1 M BIS-TRIS PROPANE PH 8.0, 1 MM TCEP, 2 MICROMETER HOMOGENTISATE, 15 MG/ML PROTEIN

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.39 α = 87.69
b = 93.71 β = 80.42
c = 162.98 γ = 68.39
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (MX-225) MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 -- BESSY 14.2

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
1.98 35 95.6 0.1 -- -- 2.9 -- 337386 -- 1.9 18.35
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)
1.98 2.03 91.5 0.59 -- 1.9 2.8 --

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 1.98 34.174 -- 1.99 -- 337340 16868 95.64 -- 0.1639 0.1611 0.2162 --
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 1.98 2.0025 -- 537 10191 0.2465 0.3105 -- 92.0
X Ray Diffraction 2.0025 2.0261 -- 541 10277 0.2308 0.2884 -- 91.0
X Ray Diffraction 2.0261 2.0508 -- 538 10252 0.2196 0.2844 -- 93.0
X Ray Diffraction 2.0508 2.0767 -- 545 10349 0.236 0.289 -- 92.0
X Ray Diffraction 2.0767 2.104 -- 540 10257 0.22 0.2882 -- 93.0
X Ray Diffraction 2.104 2.1329 -- 552 10480 0.1925 0.2608 -- 94.0
X Ray Diffraction 2.1329 2.1633 -- 553 10519 0.1952 0.2686 -- 94.0
X Ray Diffraction 2.1633 2.1956 -- 557 10567 0.1997 0.2613 -- 94.0
X Ray Diffraction 2.1956 2.2299 -- 558 10617 0.1882 0.2681 -- 95.0
X Ray Diffraction 2.2299 2.2665 -- 550 10434 0.1936 0.2732 -- 94.0
X Ray Diffraction 2.2665 2.3055 -- 559 10610 0.1751 0.2339 -- 95.0
X Ray Diffraction 2.3055 2.3474 -- 565 10749 0.1862 0.2679 -- 96.0
X Ray Diffraction 2.3474 2.3926 -- 565 10727 0.1811 0.2555 -- 96.0
X Ray Diffraction 2.3926 2.4414 -- 562 10678 0.1629 0.2251 -- 96.0
X Ray Diffraction 2.4414 2.4945 -- 565 10735 0.1798 0.2518 -- 96.0
X Ray Diffraction 2.4945 2.5525 -- 570 10836 0.1642 0.2362 -- 97.0
X Ray Diffraction 2.5525 2.6163 -- 571 10842 0.1793 0.2596 -- 97.0
X Ray Diffraction 2.6163 2.687 -- 567 10769 0.1791 0.2478 -- 97.0
X Ray Diffraction 2.687 2.766 -- 572 10876 0.1749 0.252 -- 97.0
X Ray Diffraction 2.766 2.8553 -- 570 10817 0.1621 0.2328 -- 97.0
X Ray Diffraction 2.8553 2.9573 -- 569 10821 0.1592 0.232 -- 97.0
X Ray Diffraction 2.9573 3.0756 -- 573 10882 0.1538 0.2062 -- 97.0
X Ray Diffraction 3.0756 3.2155 -- 573 10887 0.1584 0.2121 -- 97.0
X Ray Diffraction 3.2155 3.3849 -- 571 10854 0.143 0.1984 -- 97.0
X Ray Diffraction 3.3849 3.5967 -- 574 10895 0.1392 0.1836 -- 97.0
X Ray Diffraction 3.5967 3.8741 -- 570 10832 0.1339 0.1796 -- 97.0
X Ray Diffraction 3.8741 4.2633 -- 574 10913 0.1202 0.1492 -- 97.0
X Ray Diffraction 4.2633 4.8787 -- 575 10917 0.1173 0.1459 -- 98.0
X Ray Diffraction 4.8787 6.1408 -- 575 10929 0.135 0.1755 -- 98.0
X Ray Diffraction 6.1408 34.179 -- 577 10960 0.1453 0.1771 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.5888
Anisotropic B[1][2] -1.7846
Anisotropic B[1][3] -0.7527
Anisotropic B[2][2] 3.5953
Anisotropic B[2][3] 0.5927
Anisotropic B[3][3] 0.9935
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 13.877
f_angle_d 1.062
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 39512
Nucleic Acid Atoms 0
Heterogen Atoms 175
Solvent Atoms 4580

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE: 1.7.3_928) refinement
PHASER model building