X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details PEG, Ammonium Fluoride

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.77 α = 90
b = 92.36 β = 90
c = 129.93 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2014-12-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU

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
2.64 30 98.7 0.071 -- 19.022 5.4 -- 30572 -- -- 49.41
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)
2.64 2.73 99.5 0.448 -- -- 5.4 3010

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 2.64 28.938 -- 1.34 -- 30531 1446 98.33 -- 0.1851 0.1832 0.2244 --
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 2.638 2.7322 -- 143 2754 0.2459 0.3077 -- 95.0
X Ray Diffraction 2.7322 2.8415 -- 166 2868 0.2434 0.2992 -- 100.0
X Ray Diffraction 2.8415 2.9707 -- 152 2904 0.2457 0.3088 -- 99.0
X Ray Diffraction 2.9707 3.1271 -- 147 2893 0.2511 0.2907 -- 99.0
X Ray Diffraction 3.1271 3.3228 -- 129 2938 0.2387 0.2723 -- 99.0
X Ray Diffraction 3.3228 3.5789 -- 128 2909 0.2078 0.2262 -- 99.0
X Ray Diffraction 3.5789 3.9383 -- 147 2911 0.1728 0.2033 -- 99.0
X Ray Diffraction 3.9383 4.5063 -- 167 2903 0.1504 0.1963 -- 98.0
X Ray Diffraction 4.5063 5.6705 -- 131 2962 0.1504 0.2027 -- 98.0
X Ray Diffraction 5.6705 28.9401 -- 136 3043 0.1478 0.1832 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.3557
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.896
f_bond_d 0.008
f_angle_d 0.987
f_plane_restr 0.005
f_chiral_restr 0.054
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5899
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 94

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10_2152)
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing version: 11.2.05
PDB_EXTRACT data extraction version: 3.15