X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
pH 7.5
Details 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 24.46 α = 90
b = 40.06 β = 90
c = 65.41 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
PIXEL (PILATUS 2M) DECTRIS MIRRORS 2011-08-06
Diffraction Radiation
Monochromator Protocol
SI (111) DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- DIAMOND I04-1

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
1.3 25.34 98.4 0.06 -- -- 12.4 -- 16355 -- 0.0 19.15
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)
1.3 1.37 93.9 1.23 -- 2.3 12.4 --

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 1.32 25.335 -- 0.0 -- 15039 1503 95.57 -- 0.1534 0.1497 0.1848 --
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 1.3201 1.3627 -- 117 1086 0.225 0.2821 -- 85.0
X Ray Diffraction 1.3627 1.4114 -- 127 1129 0.1919 0.2955 -- 90.0
X Ray Diffraction 1.4114 1.4679 -- 130 1186 0.1629 0.22 -- 93.0
X Ray Diffraction 1.4679 1.5347 -- 134 1165 0.1396 0.1949 -- 93.0
X Ray Diffraction 1.5347 1.6156 -- 138 1234 0.113 0.2065 -- 97.0
X Ray Diffraction 1.6156 1.7168 -- 135 1249 0.1001 0.1565 -- 98.0
X Ray Diffraction 1.7168 1.8493 -- 141 1266 0.1096 0.168 -- 99.0
X Ray Diffraction 1.8493 2.0353 -- 144 1283 0.1419 0.1721 -- 99.0
X Ray Diffraction 2.0353 2.3296 -- 140 1277 0.15 0.2021 -- 99.0
X Ray Diffraction 2.3296 2.9344 -- 146 1301 0.1731 0.2427 -- 99.0
X Ray Diffraction 2.9344 25.34 -- 151 1360 0.1527 0.1554 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.89
Anisotropic B[1][1] 2.8962
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.8127
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0835
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.033
f_chiral_restr 0.113
f_dihedral_angle_d 31.124
f_angle_d 2.364
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 488
Heterogen Atoms 1
Solvent Atoms 94

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building