X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 25% (v/v) PEG 3350, 0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.2 α = 90
b = 54.2 β = 90
c = 152.2 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2005-10-22
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 0.97878, 0.97863, 0.96409 ALS 4.2.2

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
2.6 43.51 100.0 0.088 -- -- 13.4 10622 7284 -- 5.0 --
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)
2.6 2.69 100.0 0.4 -- 4.8 13.11 712

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
MAD 2.8 30.0 -- 0.0 10622 10622 1062 99.4 0.403 0.429 0.286 0.313 random
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 2.8 2.85 529 55 474 0.415 0.431 -- --
X Ray Diffraction 2.85 2.89 483 52 431 0.387 0.482 -- --
X Ray Diffraction 2.89 2.95 514 38 476 0.384 0.387 -- --
X Ray Diffraction 2.95 3.0 503 59 444 0.402 0.419 -- --
X Ray Diffraction 3.0 3.07 497 45 452 0.386 0.351 -- --
X Ray Diffraction 3.07 3.13 488 49 439 0.384 0.525 -- --
X Ray Diffraction 3.13 3.2 520 72 448 0.426 0.394 -- --
X Ray Diffraction 3.2 3.28 493 47 446 0.359 0.428 -- --
X Ray Diffraction 3.28 3.37 511 47 464 0.357 0.451 -- --
X Ray Diffraction 3.37 3.47 504 46 458 0.357 0.319 -- --
X Ray Diffraction 3.47 3.58 508 52 456 0.326 0.386 -- --
X Ray Diffraction 3.58 3.71 487 47 440 0.29 0.318 -- --
X Ray Diffraction 3.71 3.86 531 47 484 0.271 0.286 -- --
X Ray Diffraction 3.86 4.04 503 43 460 0.263 0.359 -- --
X Ray Diffraction 4.04 4.25 510 51 459 0.255 0.244 -- --
X Ray Diffraction 4.25 4.51 514 64 450 0.24 0.196 -- --
X Ray Diffraction 4.51 4.86 498 39 459 0.238 0.269 -- --
X Ray Diffraction 4.86 5.35 493 41 452 0.249 0.382 -- --
X Ray Diffraction 5.35 6.12 510 69 441 0.333 0.326 -- --
X Ray Diffraction 6.12 7.68 521 61 460 0.194 0.193 -- --
X Ray Diffraction 7.68 30.0 505 38 467 0.222 0.319 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.739
Anisotropic B[1][1] -30.976
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -30.976
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 61.952
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.008
c_angle_d 0.942
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.53
Luzzati Sigma A (Observed) 0.64
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.6
Luzzati Sigma A (R-Free Set) 0.76
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 812
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 14

Software

Software
Software Name Purpose
d*TREK data scaling version: 9.4LDz
SOLVE phasing version: 2.09
RESOLVE phasing version: 2.09
CNS refinement
PDB_EXTRACT data extraction version: 2.000
CrystalClear data collection
d*TREK data reduction