X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.6
Temperature 293.0
Details 35% (v/v) PEG 400, ADA pH 6.6 and 0.1 M Potassium phosphate monobasic., VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.01 α = 90
b = 142.01 β = 90
c = 251.75 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2008-01-01
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.08 SSRL BL12-2

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
6.8 125.87 95.9 -- 0.048 -- 6.8 2281 2281 40.25 8.37 --
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)
6.8 7.17 96.9 0.79 0.79 0.9 7.0 326

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 6.8 30.0 -- 3.1 2385 2262 98 95.2 0.3437 0.3437 0.3437 0.4182 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 6.8 7.04 -- 7 211 0.3898 0.3361 -- 96.0
X Ray Diffraction 7.04 7.32 -- 9 215 0.3565 0.4279 -- 95.7
X Ray Diffraction 7.32 7.65 -- 10 209 0.3444 0.608 -- 95.2
X Ray Diffraction 7.65 8.04 -- 11 219 0.3105 0.3797 -- 95.8
X Ray Diffraction 8.04 8.53 -- 11 207 0.2818 0.3411 -- 96.0
X Ray Diffraction 8.53 9.18 -- 7 218 0.2175 0.2869 -- 95.3
X Ray Diffraction 9.18 10.07 -- 10 216 0.2359 0.3012 -- 95.0
X Ray Diffraction 10.07 11.45 -- 7 212 0.3095 0.5757 -- 94.0
X Ray Diffraction 11.45 14.17 -- 14 224 0.3561 0.3048 -- 95.2
X Ray Diffraction 14.17 30.0 -- 12 233 0.4371 0.5568 -- 93.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 474.471
Anisotropic B[1][1] 67.644
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 67.644
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -135.289
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 26.356
c_bond_d 0.004
c_angle_d 0.931
c_scbond_it 17.912
c_mcangle_it 28.028
c_mcbond_it 18.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3608
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
XDS data reduction
CNS refinement