X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.77 α = 90
b = 402.77 β = 90
c = 177.09 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-11-07
Diffraction Radiation
Monochromator Protocol
KOHZU HLD8-24 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.01 35 96.4 0.064 -- -- 3.3 274619 274619 -3.0 -3.0 --
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)
3.009 3.12 98.8 0.771 -- -- 3.3 27865

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
FOURIER SYNTHESIS 3.009 34.537 -- 1.34 274463 274463 13977 96.45 0.1711 0.1711 0.1694 0.2034 FROM PDB ENTRY 2VQE
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 3.009 3.0432 -- 479 8817 0.3447 0.3758 -- 99.0
X Ray Diffraction 3.0432 3.079 -- 483 8811 0.3109 0.3506 -- 99.0
X Ray Diffraction 3.079 3.1165 -- 496 8764 0.2792 0.2817 -- 98.0
X Ray Diffraction 3.1165 3.1559 -- 471 8821 0.2659 0.292 -- 99.0
X Ray Diffraction 3.1559 3.1974 -- 523 8778 0.2537 0.2892 -- 99.0
X Ray Diffraction 3.1974 3.2412 -- 478 8789 0.2472 0.2834 -- 99.0
X Ray Diffraction 3.2412 3.2874 -- 479 8819 0.2301 0.2697 -- 99.0
X Ray Diffraction 3.2874 3.3365 -- 480 8817 0.2154 0.2441 -- 99.0
X Ray Diffraction 3.3365 3.3886 -- 475 8835 0.2019 0.2451 -- 99.0
X Ray Diffraction 3.3886 3.4441 -- 467 8799 0.1964 0.2296 -- 99.0
X Ray Diffraction 3.4441 3.5034 -- 493 8768 0.1943 0.2363 -- 98.0
X Ray Diffraction 3.5034 3.567 -- 519 8756 0.1838 0.2162 -- 98.0
X Ray Diffraction 3.567 3.6356 -- 466 8784 0.1751 0.2108 -- 98.0
X Ray Diffraction 3.6356 3.7097 -- 480 8776 0.1617 0.187 -- 98.0
X Ray Diffraction 3.7097 3.7903 -- 486 8777 0.1565 0.1924 -- 98.0
X Ray Diffraction 3.7903 3.8783 -- 417 8789 0.1495 0.1853 -- 98.0
X Ray Diffraction 3.8783 3.9752 -- 460 8775 0.1504 0.1959 -- 98.0
X Ray Diffraction 3.9752 4.0825 -- 492 8734 0.147 0.1797 -- 98.0
X Ray Diffraction 4.0825 4.2024 -- 451 8723 0.1398 0.174 -- 97.0
X Ray Diffraction 4.2024 4.3378 -- 455 8739 0.1386 0.1825 -- 97.0
X Ray Diffraction 4.3378 4.4925 -- 489 8665 0.1354 0.164 -- 97.0
X Ray Diffraction 4.4925 4.672 -- 454 8684 0.1364 0.1802 -- 96.0
X Ray Diffraction 4.672 4.8841 -- 415 8699 0.1377 0.1713 -- 96.0
X Ray Diffraction 4.8841 5.1408 -- 460 8573 0.1353 0.1757 -- 95.0
X Ray Diffraction 5.1408 5.4617 -- 438 8586 0.1345 0.1841 -- 94.0
X Ray Diffraction 5.4617 5.8815 -- 453 8522 0.1402 0.1755 -- 94.0
X Ray Diffraction 5.8815 6.4699 -- 409 8535 0.1503 0.1777 -- 93.0
X Ray Diffraction 6.4699 7.3981 -- 446 8407 0.1467 0.1825 -- 92.0
X Ray Diffraction 7.3981 9.2907 -- 438 8246 0.1665 0.1907 -- 89.0
X Ray Diffraction 9.2907 34.5391 -- 425 7898 0.2205 0.2372 -- 83.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 102.318
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_bond_d 0.004
f_dihedral_angle_d 16.695
f_chiral_restr 0.047
f_angle_d 0.785
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19153
Nucleic Acid Atoms 32504
Heterogen Atoms 365
Solvent Atoms 24

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
PHENIX phasing