X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details PEG 5000, potassium chloride, magnesium chloride, PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.36 α = 90
b = 57.92 β = 101.57
c = 101.28 γ = 90
Symmetry
Space Group P 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2015-07-06
Diffraction Radiation
Monochromator Protocol
Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.972420 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
2.19 46.02 97.5 0.143 -- -- 5.6 -- 44173 -- -- --
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)
2.19 2.31 90.4 1.135 -- 1.2 5.6 --

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 2.195 45.945 -- 0.0 -- 85430 2458 96.98 -- 0.2521 0.2508 0.2965 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 2.195 2.2372 -- 87 3770 0.3943 0.3641 -- 78.0
X Ray Diffraction 2.2372 2.2829 -- 160 4666 0.3487 0.3554 -- 99.0
X Ray Diffraction 2.2829 2.3325 -- 144 4572 0.3444 0.4682 -- 97.0
X Ray Diffraction 2.3325 2.3867 -- 125 4664 0.3118 0.316 -- 98.0
X Ray Diffraction 2.3867 2.4464 -- 132 4629 0.3024 0.3517 -- 98.0
X Ray Diffraction 2.4464 2.5126 -- 154 4653 0.2971 0.3886 -- 97.0
X Ray Diffraction 2.5126 2.5865 -- 130 4710 0.2933 0.3366 -- 99.0
X Ray Diffraction 2.5865 2.67 -- 135 4673 0.2788 0.302 -- 98.0
X Ray Diffraction 2.67 2.7654 -- 136 4658 0.3008 0.3821 -- 98.0
X Ray Diffraction 2.7654 2.8761 -- 141 4679 0.3001 0.4258 -- 99.0
X Ray Diffraction 2.8761 3.007 -- 140 4688 0.2722 0.3771 -- 98.0
X Ray Diffraction 3.007 3.1655 -- 168 4610 0.2625 0.3256 -- 98.0
X Ray Diffraction 3.1655 3.3637 -- 140 4562 0.233 0.2758 -- 96.0
X Ray Diffraction 3.3637 3.6234 -- 126 4635 0.21 0.2713 -- 97.0
X Ray Diffraction 3.6234 3.9878 -- 135 4698 0.2217 0.2568 -- 99.0
X Ray Diffraction 3.9878 4.5644 -- 129 4731 0.2196 0.2435 -- 99.0
X Ray Diffraction 4.5644 5.7489 -- 139 4743 0.2072 0.2215 -- 100.0
X Ray Diffraction 5.7489 45.9551 -- 137 4631 0.2095 0.2476 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.264
f_dihedral_angle_d 28.466
f_bond_d 0.011
f_chiral_restr 0.076
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2103
Nucleic Acid Atoms 2949
Heterogen Atoms 0
Solvent Atoms 518

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
SCALA data scaling
PHASER phasing