X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
Temperature 291.0
Details 4.3% PEG 8000, 4.9% MPD, 10 mM Tris, 20 mM MES, pH 6.5-7.0, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 0.25 mM EDTA, microbatch, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 211.08 α = 90
b = 434.46 β = 90
c = 618.92 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 ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.11589 ALS 8.3.1

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
3.29 80 83.2 0.12 -- -- 6.3 700416 700416 1.68 1.68 --
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)
3.289 3.38 70.6 0.743 -- -- 4.4 --

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 3.2891 76.348 -- 0.05 661143 661143 13296 77.52 -- 0.1897 0.1887 0.241 --
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 3.2891 3.3265 -- 209 11632 0.2965 0.3178 -- 42.0
X Ray Diffraction 3.3265 3.3656 -- 315 16406 0.2806 0.3343 -- 59.0
X Ray Diffraction 3.3656 3.4067 -- 350 16961 0.2674 0.3347 -- 61.0
X Ray Diffraction 3.4067 3.4498 -- 364 17067 0.2596 0.3102 -- 62.0
X Ray Diffraction 3.4498 3.4952 -- 379 17366 0.2431 0.3077 -- 63.0
X Ray Diffraction 3.4952 3.5431 -- 366 17951 0.2315 0.2766 -- 65.0
X Ray Diffraction 3.5431 3.5937 -- 365 18338 0.2272 0.2745 -- 66.0
X Ray Diffraction 3.5937 3.6473 -- 394 18648 0.219 0.2715 -- 67.0
X Ray Diffraction 3.6473 3.7043 -- 359 19133 0.208 0.2659 -- 69.0
X Ray Diffraction 3.7043 3.765 -- 418 19350 0.2051 0.2486 -- 70.0
X Ray Diffraction 3.765 3.83 -- 393 19678 0.1931 0.237 -- 71.0
X Ray Diffraction 3.83 3.8996 -- 404 20173 0.1896 0.2526 -- 73.0
X Ray Diffraction 3.8996 3.9746 -- 405 20491 0.1822 0.2325 -- 74.0
X Ray Diffraction 3.9746 4.0557 -- 445 20854 0.1845 0.2351 -- 75.0
X Ray Diffraction 4.0557 4.1439 -- 424 21320 0.1825 0.2251 -- 77.0
X Ray Diffraction 4.1439 4.2403 -- 417 21692 0.1812 0.2369 -- 78.0
X Ray Diffraction 4.2403 4.3463 -- 493 22352 0.1816 0.2316 -- 81.0
X Ray Diffraction 4.3463 4.4638 -- 448 23169 0.1737 0.2368 -- 83.0
X Ray Diffraction 4.4638 4.5952 -- 504 23728 0.1678 0.2271 -- 85.0
X Ray Diffraction 4.5952 4.7435 -- 517 24362 0.1668 0.226 -- 88.0
X Ray Diffraction 4.7435 4.913 -- 526 24896 0.1751 0.2198 -- 89.0
X Ray Diffraction 4.913 5.1096 -- 527 24972 0.1678 0.2347 -- 90.0
X Ray Diffraction 5.1096 5.3421 -- 508 25179 0.1628 0.2283 -- 90.0
X Ray Diffraction 5.3421 5.6237 -- 505 25352 0.1622 0.2231 -- 91.0
X Ray Diffraction 5.6237 5.9759 -- 523 25503 0.1647 0.232 -- 91.0
X Ray Diffraction 5.9759 6.4371 -- 553 25676 0.1716 0.253 -- 92.0
X Ray Diffraction 6.4371 7.0845 -- 538 25976 0.1604 0.2208 -- 93.0
X Ray Diffraction 7.0845 8.1086 -- 562 26290 0.1682 0.2123 -- 93.0
X Ray Diffraction 8.1086 10.2121 -- 533 26565 0.1839 0.2277 -- 94.0
X Ray Diffraction 10.2121 76.3689 -- 552 26767 0.2059 0.2284 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.387
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -9.5112
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.221
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.382
f_bond_d 0.006
f_dihedral_angle_d 27.993
f_chiral_restr 0.075
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 89372
Nucleic Acid Atoms 193031
Heterogen Atoms 390
Solvent Atoms 1708

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.10
PHENIX refinement version: (phenix.refine)