X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.15
Details 100 mM TRIS, 1 mM DTT, 10 % DMSO, 12 % PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.36 α = 90
b = 64.89 β = 95.82
c = 70.38 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113.15
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirror 2010-12-15
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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
1.18 30 95.0 -- -- -- 2.5 125858 125858 -- -- 10.42
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)
1.18 1.2 88.0 -- 0.218 4.13 2.2 5750

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 1.18 21.031 -- 1.0 121156 121156 12053 91.49 -- 0.1391 0.1375 0.1528 Random,10%
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 1.1804 1.1938 -- 376 3062 0.1686 0.2015 -- 79.0
X Ray Diffraction 1.1938 1.2079 -- 393 3309 0.1565 0.18 -- 84.0
X Ray Diffraction 1.2079 1.2226 -- 378 3329 0.1525 0.1612 -- 85.0
X Ray Diffraction 1.2226 1.2381 -- 373 3426 0.1468 0.162 -- 86.0
X Ray Diffraction 1.2381 1.2544 -- 354 3440 0.137 0.1617 -- 86.0
X Ray Diffraction 1.2544 1.2716 -- 413 3418 0.132 0.1684 -- 87.0
X Ray Diffraction 1.2716 1.2897 -- 378 3512 0.1266 0.1412 -- 88.0
X Ray Diffraction 1.2897 1.309 -- 407 3519 0.116 0.1456 -- 89.0
X Ray Diffraction 1.309 1.3294 -- 386 3608 0.1158 0.147 -- 90.0
X Ray Diffraction 1.3294 1.3512 -- 356 3663 0.1103 0.1329 -- 91.0
X Ray Diffraction 1.3512 1.3745 -- 414 3522 0.1093 0.1204 -- 90.0
X Ray Diffraction 1.3745 1.3995 -- 407 3624 0.1084 0.1307 -- 92.0
X Ray Diffraction 1.3995 1.4264 -- 383 3706 0.1037 0.1255 -- 92.0
X Ray Diffraction 1.4264 1.4555 -- 438 3698 0.1058 0.1285 -- 93.0
X Ray Diffraction 1.4555 1.4872 -- 413 3629 0.0998 0.1231 -- 93.0
X Ray Diffraction 1.4872 1.5217 -- 425 3706 0.0993 0.1281 -- 94.0
X Ray Diffraction 1.5217 1.5598 -- 441 3766 0.1017 0.1234 -- 95.0
X Ray Diffraction 1.5598 1.602 -- 401 3806 0.1004 0.1269 -- 96.0
X Ray Diffraction 1.602 1.6491 -- 420 3802 0.1036 0.1199 -- 96.0
X Ray Diffraction 1.6491 1.7023 -- 427 3812 0.1081 0.1384 -- 96.0
X Ray Diffraction 1.7023 1.7631 -- 413 3835 0.1155 0.1364 -- 97.0
X Ray Diffraction 1.7631 1.8336 -- 397 3881 0.1204 0.1368 -- 97.0
X Ray Diffraction 1.8336 1.917 -- 407 3926 0.1253 0.1397 -- 97.0
X Ray Diffraction 1.917 2.018 -- 443 3821 0.1323 0.1487 -- 97.0
X Ray Diffraction 2.018 2.1444 -- 434 3944 0.1401 0.1569 -- 98.0
X Ray Diffraction 2.1444 2.3097 -- 417 3917 0.1395 0.1583 -- 98.0
X Ray Diffraction 2.3097 2.5418 -- 423 3962 0.1425 0.1555 -- 99.0
X Ray Diffraction 2.5418 2.9088 -- 437 3966 0.1533 0.1527 -- 99.0
X Ray Diffraction 2.9088 3.6616 -- 387 3732 0.1564 0.1536 -- 93.0
X Ray Diffraction 3.6616 21.0344 -- 312 2762 0.2082 0.2269 -- 68.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Anisotropic B[1][1] 0.1179
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.0946
Anisotropic B[2][2] -0.5328
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4149
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.076
f_dihedral_angle_d 12.643
f_angle_d 1.202
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2810
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 464

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Paser Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
Paser model building
HKL-2000 data collection