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 = 85.67 α = 90
b = 91.43 β = 90
c = 128.37 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
IMAGE PLATE MAR scanner 300 mm plate -- 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
2.7 30 97.6 0.066 -- 24.783 6.0 -- 27758 -- -- 66.05
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)
2.7 2.8 99.2 0.609 -- -- 6.2 2762

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 2.7 28.74 -- 1.33 -- 27716 1403 97.53 -- 0.19 0.1886 0.2159 Random selection
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 2.6973 2.7936 -- 146 2592 0.2764 0.3102 -- 98.0
X Ray Diffraction 2.7936 2.9054 -- 147 2632 0.25 0.2831 -- 99.0
X Ray Diffraction 2.9054 3.0375 -- 139 2626 0.24 0.2753 -- 99.0
X Ray Diffraction 3.0375 3.1974 -- 140 2636 0.2384 0.2598 -- 99.0
X Ray Diffraction 3.1974 3.3974 -- 130 2631 0.2159 0.2556 -- 98.0
X Ray Diffraction 3.3974 3.6593 -- 123 2664 0.201 0.2266 -- 98.0
X Ray Diffraction 3.6593 4.0266 -- 147 2627 0.1718 0.1966 -- 98.0
X Ray Diffraction 4.0266 4.6072 -- 151 2609 0.1585 0.1929 -- 97.0
X Ray Diffraction 4.6072 5.7968 -- 123 2654 0.1694 0.1899 -- 96.0
X Ray Diffraction 5.7968 28.7412 -- 157 2642 0.1756 0.2001 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.555
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.022
f_bond_d 0.007
f_angle_d 0.687
f_plane_restr 0.004
f_chiral_restr 0.041
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5856
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 106

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10_2152
DENZO data collection
SCALEPACK data scaling
MOLREP phasing
PDB_EXTRACT data extraction version: 3.15