X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.9 α = 90
b = 52.56 β = 90
c = 89.41 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 278
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-04-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.100 SSRL BL7-1

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
1.49 38.68 85.9 0.109 -- -- 2.8 -- 28617 -- -- 17.26
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)
1.49 1.52 65.1 0.526 -- -- 2.3 --

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 1.7 34.053 -- 1.34 -- 20749 1060 90.58 -- 0.1548 0.1532 0.1844 --
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 1.7001 1.7774 -- 128 2390 0.2182 0.271 -- 90.0
X Ray Diffraction 1.7774 1.8711 -- 125 2406 0.1893 0.2242 -- 90.0
X Ray Diffraction 1.8711 1.9884 -- 136 2387 0.1708 0.1945 -- 90.0
X Ray Diffraction 1.9884 2.1419 -- 135 2394 0.1601 0.2023 -- 89.0
X Ray Diffraction 2.1419 2.3574 -- 141 2461 0.1497 0.1711 -- 91.0
X Ray Diffraction 2.3574 2.6983 -- 129 2499 0.1644 0.1929 -- 92.0
X Ray Diffraction 2.6983 3.3991 -- 145 2503 0.1536 0.1865 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.0504
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 0.784
f_chiral_restr 0.06
f_dihedral_angle_d 10.513
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1258
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 127

Software

Software
Software Name Purpose
Blu-Ice data collection
XDS data reduction
Aimless data scaling version: 0.1.26
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.20