X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.02 α = 90
b = 66.67 β = 94.02
c = 64.92 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-12-08
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.12 ALS 12.3.1

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
1.63 25 99.2 0.063 -- -- 4.9 40567 40567 0.0 -3.0 --
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)
1.63 1.67 99.5 0.595 -- 2.2 5.0 2989

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 1.63 22.92 -- 1.34 -- 40565 1998 99.14 -- 0.1935 0.1918 0.2273 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 1.63 1.6708 -- 169 2717 0.2649 0.3036 -- 100.0
X Ray Diffraction 1.6708 1.7159 -- 142 2743 0.2609 0.3119 -- 100.0
X Ray Diffraction 1.7159 1.7664 -- 136 2782 0.2559 0.2948 -- 99.0
X Ray Diffraction 1.7664 1.8234 -- 151 2745 0.2499 0.289 -- 100.0
X Ray Diffraction 1.8234 1.8885 -- 115 2759 0.2272 0.2668 -- 100.0
X Ray Diffraction 1.8885 1.9641 -- 174 2764 0.2106 0.2506 -- 99.0
X Ray Diffraction 1.9641 2.0534 -- 147 2708 0.2009 0.2544 -- 100.0
X Ray Diffraction 2.0534 2.1616 -- 108 2801 0.1885 0.2047 -- 99.0
X Ray Diffraction 2.1616 2.2969 -- 153 2746 0.1869 0.2349 -- 99.0
X Ray Diffraction 2.2969 2.4741 -- 153 2734 0.1834 0.2271 -- 99.0
X Ray Diffraction 2.4741 2.7227 -- 144 2744 0.1857 0.2243 -- 99.0
X Ray Diffraction 2.7227 3.1159 -- 114 2813 0.187 0.2104 -- 99.0
X Ray Diffraction 3.1159 3.9225 -- 149 2797 0.1695 0.223 -- 100.0
X Ray Diffraction 3.9225 22.9224 -- 143 2714 0.1859 0.198 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.9075
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -4.0202
Anisotropic B[2][2] 5.6611
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7536
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.011
f_plane_restr 0.006
f_angle_d 1.258
f_dihedral_angle_d 13.096
f_chiral_restr 0.073
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1859
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 250

Software

Software
Software Name Purpose
Blu-Ice data collection version: Ice
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
XDS data reduction version: (xia2)
XDS data scaling version: (xia2
SCALA data scaling