X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 DECTRIS PILATUS 2M 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_bond_d 0.021
f_chiral_restr 0.113
f_dihedral_angle_d 31.124
f_angle_d 2.364
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
SCALA data scaling
PHASER phasing