X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.1
Temperature 298.15
Details 50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 334.67 α = 90
b = 597.13 β = 120.29
c = 336.5 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2016-08-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 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
6 120 99.4 -- -- -- 6.8 -- 282736 -- -- --
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)
-- -- -- -- -- -- -- --

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 6.0 116.931 -- 1.34 -- 281673 14432 99.33 -- 0.3227 0.3228 0.3207 --
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 6.0 6.0682 -- 494 8414 0.3901 0.3829 0.0 95.0
X Ray Diffraction 6.0682 6.1396 -- 440 8483 0.3922 0.4055 0.0 95.0
X Ray Diffraction 6.1396 6.2144 -- 405 9009 0.3873 0.3731 0.0 99.0
X Ray Diffraction 6.2144 6.2931 -- 449 8922 0.3916 0.3884 0.0 100.0
X Ray Diffraction 6.2931 6.3759 -- 470 8889 0.3974 0.3943 0.0 100.0
X Ray Diffraction 6.3759 6.4632 -- 464 9037 0.4026 0.4194 0.0 100.0
X Ray Diffraction 6.4632 6.5556 -- 443 8974 0.3964 0.3899 0.0 100.0
X Ray Diffraction 6.5556 6.6534 -- 505 8887 0.3908 0.3858 0.0 100.0
X Ray Diffraction 6.6534 6.7574 -- 472 8927 0.3921 0.3938 0.0 100.0
X Ray Diffraction 6.7574 6.8681 -- 484 8985 0.3919 0.4137 0.0 100.0
X Ray Diffraction 6.8681 6.9865 -- 448 8999 0.3911 0.3569 0.0 100.0
X Ray Diffraction 6.9865 7.1136 -- 512 8940 0.3837 0.3951 0.0 100.0
X Ray Diffraction 7.1136 7.2504 -- 459 8948 0.3809 0.3737 0.0 100.0
X Ray Diffraction 7.2504 7.3983 -- 537 8851 0.3842 0.3833 0.0 100.0
X Ray Diffraction 7.3983 7.5592 -- 534 8937 0.3856 0.3729 0.0 100.0
X Ray Diffraction 7.5592 7.735 -- 506 8873 0.3775 0.3638 0.0 100.0
X Ray Diffraction 7.735 7.9284 -- 446 9006 0.3755 0.3544 0.0 100.0
X Ray Diffraction 7.9284 8.1427 -- 507 8790 0.375 0.3457 0.0 98.0
X Ray Diffraction 8.1427 8.3822 -- 595 8829 0.3706 0.3765 0.0 100.0
X Ray Diffraction 8.3822 8.6527 -- 487 8942 0.3571 0.3788 0.0 100.0
X Ray Diffraction 8.6527 8.9619 -- 403 9036 0.3568 0.3827 0.0 100.0
X Ray Diffraction 8.9619 9.3205 -- 486 8974 0.352 0.3501 0.0 100.0
X Ray Diffraction 9.3205 9.7445 -- 590 8839 0.3356 0.3362 0.0 100.0
X Ray Diffraction 9.7445 10.258 -- 476 8997 0.318 0.3512 0.0 100.0
X Ray Diffraction 10.258 10.9003 -- 470 8979 0.2987 0.2926 0.0 100.0
X Ray Diffraction 10.9003 11.7412 -- 435 8995 0.2926 0.2789 0.0 100.0
X Ray Diffraction 11.7412 12.9214 -- 416 8973 0.2921 0.2771 0.0 98.0
X Ray Diffraction 12.9214 14.788 -- 441 8983 0.3016 0.3104 0.0 100.0
X Ray Diffraction 14.788 18.6191 -- 542 8950 0.2857 0.276 0.0 99.0
X Ray Diffraction 18.6191 116.954 -- 516 8873 0.2306 0.239 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 204.98
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.034
f_bond_d 0.01
f_dihedral_angle_d 16.998
f_angle_d 0.999
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 249168
Nucleic Acid Atoms 221400
Heterogen Atoms 6
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing