X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.1 α = 90
b = 153.67 β = 90
c = 52.5 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r bent cylindrical mirror 2011-02-28
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97917 ESRF ID23-1

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
1.8 20 99.1 0.114 -- -- 5.2 59555 59045 -- -3.0 22.143
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)
1.8 1.9 99.4 0.655 -- 2.45 5.3 8789

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 1.8 19.937 -- 1.99 -- 58994 1771 99.27 -- 0.1524 0.1512 0.1906 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 1.8 1.8487 4502 135 4367 0.2303 0.2783 -- 99.0
X Ray Diffraction 1.8487 1.903 4447 134 4313 0.2054 0.2592 -- 99.0
X Ray Diffraction 1.903 1.9644 4501 135 4366 0.1778 0.2307 -- 100.0
X Ray Diffraction 1.9644 2.0345 4508 135 4373 0.1616 0.1979 -- 100.0
X Ray Diffraction 2.0345 2.1159 4505 135 4370 0.1472 0.1878 -- 100.0
X Ray Diffraction 2.1159 2.2121 4500 136 4364 0.1443 0.1856 -- 100.0
X Ray Diffraction 2.2121 2.3285 4521 135 4386 0.1396 0.1635 -- 100.0
X Ray Diffraction 2.3285 2.4742 4560 137 4423 0.1508 0.2019 -- 100.0
X Ray Diffraction 2.4742 2.6648 4550 137 4413 0.1422 0.2064 -- 100.0
X Ray Diffraction 2.6648 2.9322 4563 137 4426 0.1549 0.1942 -- 100.0
X Ray Diffraction 2.9322 3.3548 4559 136 4423 0.1411 0.1743 -- 99.0
X Ray Diffraction 3.3548 4.2201 4582 137 4445 0.1278 0.1608 -- 98.0
X Ray Diffraction 4.2201 19.938 4696 142 4554 0.1497 0.1775 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 17.0653
Anisotropic B[1][1] -0.063
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1133
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1763
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.993
f_plane_restr 0.006
f_chiral_restr 0.083
f_angle_d 1.208
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4868
Nucleic Acid Atoms 0
Heterogen Atoms 140
Solvent Atoms 631

Software

Computing
Computing Package Purpose
mxCuBE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction