X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 291.0
Details 5% MPD, 10-12% PEG 6000, and 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140 α = 90
b = 147.31 β = 90
c = 238.49 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 -- 2006-07-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1

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
3.2 147.44 99.4 0.11 0.11 -- 4.0 -- 81299 -- -- --
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)
3.2 3.28 100.0 0.831 0.831 0.9 4.1 5966

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 3.2 30.0 -- 277.0 -- 80849 4058 98.8 -- -- 0.233 0.311 --
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 3.2 3.22 1572 76 1496 0.349 0.389 -- --
X Ray Diffraction 3.22 3.24 1573 98 1475 0.341 0.364 -- --
X Ray Diffraction 3.24 3.27 1616 88 1528 0.353 0.376 -- --
X Ray Diffraction 3.27 3.29 1598 87 1511 0.343 0.385 -- --
X Ray Diffraction 3.29 3.31 1561 72 1489 0.339 0.437 -- --
X Ray Diffraction 3.31 3.34 1649 77 1572 0.339 0.354 -- --
X Ray Diffraction 3.34 3.36 1585 85 1500 0.32 0.371 -- --
X Ray Diffraction 3.36 3.39 1582 73 1509 0.308 0.357 -- --
X Ray Diffraction 3.39 3.42 1620 71 1549 0.33 0.379 -- --
X Ray Diffraction 3.42 3.45 1615 80 1535 0.336 0.444 -- --
X Ray Diffraction 3.45 3.48 1591 78 1513 0.316 0.415 -- --
X Ray Diffraction 3.48 3.51 1654 92 1562 0.295 0.35 -- --
X Ray Diffraction 3.51 3.54 1575 88 1487 0.285 0.316 -- --
X Ray Diffraction 3.54 3.57 1592 79 1513 0.281 0.327 -- --
X Ray Diffraction 3.57 3.6 1645 75 1570 0.287 0.368 -- --
X Ray Diffraction 3.6 3.64 1615 81 1534 0.282 0.319 -- --
X Ray Diffraction 3.64 3.67 1627 95 1532 0.288 0.377 -- --
X Ray Diffraction 3.67 3.71 1583 83 1500 0.275 0.344 -- --
X Ray Diffraction 3.71 3.75 1616 74 1542 0.279 0.346 -- --
X Ray Diffraction 3.75 3.79 1641 88 1553 0.286 0.315 -- --
X Ray Diffraction 3.79 3.84 1607 61 1546 0.24 0.348 -- --
X Ray Diffraction 3.84 3.88 1616 83 1533 0.264 0.349 -- --
X Ray Diffraction 3.88 3.93 1607 91 1516 0.279 0.354 -- --
X Ray Diffraction 3.93 3.98 1629 66 1563 0.256 0.321 -- --
X Ray Diffraction 3.98 4.03 1600 90 1510 0.257 0.347 -- --
X Ray Diffraction 4.03 4.09 1625 71 1554 0.259 0.342 -- --
X Ray Diffraction 4.09 4.14 1624 78 1546 0.25 0.315 -- --
X Ray Diffraction 4.14 4.21 1621 84 1537 0.222 0.324 -- --
X Ray Diffraction 4.21 4.27 1590 89 1501 0.229 0.323 -- --
X Ray Diffraction 4.27 4.34 1639 70 1569 0.202 0.301 -- --
X Ray Diffraction 4.34 4.42 1622 67 1555 0.225 0.325 -- --
X Ray Diffraction 4.42 4.5 1618 91 1527 0.214 0.361 -- --
X Ray Diffraction 4.5 4.58 1602 84 1518 0.224 0.357 -- --
X Ray Diffraction 4.58 4.67 1628 76 1552 0.21 0.312 -- --
X Ray Diffraction 4.67 4.78 1619 89 1530 0.205 0.276 -- --
X Ray Diffraction 4.78 4.89 1604 83 1521 0.219 0.319 -- --
X Ray Diffraction 4.89 5.01 1624 72 1552 0.196 0.255 -- --
X Ray Diffraction 5.01 5.14 1616 78 1538 0.189 0.24 -- --
X Ray Diffraction 5.14 5.29 1635 88 1547 0.213 0.333 -- --
X Ray Diffraction 5.29 5.46 1621 74 1547 0.194 0.261 -- --
X Ray Diffraction 5.46 5.66 1638 91 1547 0.234 0.348 -- --
X Ray Diffraction 5.66 5.88 1607 84 1523 0.24 0.346 -- --
X Ray Diffraction 5.88 6.15 1659 76 1583 0.258 0.369 -- --
X Ray Diffraction 6.15 6.47 1607 81 1526 0.239 0.331 -- --
X Ray Diffraction 6.47 6.87 1613 86 1527 0.239 0.357 -- --
X Ray Diffraction 6.87 7.39 1634 86 1548 0.189 0.295 -- --
X Ray Diffraction 7.39 8.12 1619 77 1542 0.179 0.28 -- --
X Ray Diffraction 8.12 9.27 1635 95 1540 0.15 0.187 -- --
X Ray Diffraction 9.27 11.56 1684 82 1602 0.166 0.258 -- --
X Ray Diffraction 11.56 30.0 1696 75 1621 0.253 0.267 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 111.396
Anisotropic B[1][1] -9.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.669
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.881
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.142
c_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26138
Nucleic Acid Atoms 0
Heterogen Atoms 385
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
CNS refinement
Phaser molecular replacement
SCALA data processing