X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 289.0
Details 1.6 M Na-Acetate, 0.1 M Na-Citrate, pH 6.5, vapor diffusion, hanging drop, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.16 α = 90
b = 68.79 β = 90
c = 90.04 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
-- -- -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.39 60 99.8 0.058 -- -- 4.9 -- 77074 -- -- --
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)
1.395 1.42 100.0 0.638 -- -- 4.1 3829

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
SAD 1.395 37.67 -- 1.36 77074 77006 7698 99.47 -- 0.1657 0.1645 0.1773 --
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 1.395 1.4113 -- 226 2049 0.3158 0.3285 -- 89.0
X Ray Diffraction 1.4113 1.4279 -- 254 2280 0.3024 0.3231 -- 100.0
X Ray Diffraction 1.4279 1.4453 -- 255 2306 0.2745 0.2844 -- 100.0
X Ray Diffraction 1.4453 1.4636 -- 254 2275 0.2464 0.2708 -- 100.0
X Ray Diffraction 1.4636 1.4828 -- 256 2306 0.2297 0.2608 -- 100.0
X Ray Diffraction 1.4828 1.5031 -- 256 2302 0.2167 0.2381 -- 100.0
X Ray Diffraction 1.5031 1.5246 -- 255 2299 0.2082 0.2306 -- 100.0
X Ray Diffraction 1.5246 1.5474 -- 254 2280 0.1911 0.2113 -- 100.0
X Ray Diffraction 1.5474 1.5715 -- 255 2297 0.1822 0.2154 -- 100.0
X Ray Diffraction 1.5715 1.5973 -- 258 2323 0.177 0.2007 -- 100.0
X Ray Diffraction 1.5973 1.6249 -- 253 2268 0.1685 0.1907 -- 100.0
X Ray Diffraction 1.6249 1.6544 -- 255 2298 0.1569 0.1827 -- 100.0
X Ray Diffraction 1.6544 1.6862 -- 258 2323 0.1606 0.1924 -- 100.0
X Ray Diffraction 1.6862 1.7206 -- 257 2310 0.1549 0.1761 -- 100.0
X Ray Diffraction 1.7206 1.7581 -- 253 2279 0.1565 0.1791 -- 100.0
X Ray Diffraction 1.7581 1.799 -- 258 2322 0.1595 0.1724 -- 100.0
X Ray Diffraction 1.799 1.8439 -- 255 2294 0.1588 0.1738 -- 100.0
X Ray Diffraction 1.8439 1.8938 -- 259 2334 0.1607 0.183 -- 100.0
X Ray Diffraction 1.8938 1.9495 -- 256 2300 0.1569 0.1821 -- 100.0
X Ray Diffraction 1.9495 2.0124 -- 255 2298 0.1561 0.1678 -- 100.0
X Ray Diffraction 2.0124 2.0844 -- 260 2336 0.1591 0.1718 -- 100.0
X Ray Diffraction 2.0844 2.1678 -- 256 2306 0.1556 0.1791 -- 100.0
X Ray Diffraction 2.1678 2.2665 -- 260 2344 0.1483 0.153 -- 100.0
X Ray Diffraction 2.2665 2.3859 -- 259 2333 0.1414 0.1575 -- 100.0
X Ray Diffraction 2.3859 2.5354 -- 258 2326 0.1479 0.166 -- 100.0
X Ray Diffraction 2.5354 2.7311 -- 263 2361 0.158 0.1729 -- 100.0
X Ray Diffraction 2.7311 3.0058 -- 262 2354 0.1672 0.1872 -- 100.0
X Ray Diffraction 3.0058 3.4405 -- 263 2375 0.1636 0.1714 -- 100.0
X Ray Diffraction 3.4405 4.3337 -- 264 2385 0.1489 0.1474 -- 100.0
X Ray Diffraction 4.3337 37.67 -- 271 2445 0.1754 0.1832 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.4023
Anisotropic B[1][1] 0.657
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.1565
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8135
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.406
f_plane_restr 0.005
f_chiral_restr 0.056
f_angle_d 1.017
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2541
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 479

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
HKL2MAP Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction