X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 295.0
Details 1.6M AmSO4, 0.1M Na Citrate pH 4.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.46 α = 90
b = 49.46 β = 90
c = 103.23 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r mirrors 2008-04-22
Diffraction Radiation
Monochromator Protocol
double mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9567 AUSTRALIAN SYNCHROTRON MX1

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
1.7 50 99.5 0.047 0.033 -- 5.6 31059 30896 2.0 -- 21.95
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)
1.7 1.8 99.5 0.29 0.308 6.15 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 1.7 26.826 -- 1.99 31051 30890 1543 99.48 0.2044 0.1995 0.1984 0.2215 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 1.7001 1.755 -- 140 2672 0.2648 0.2988 -- 100.0
X Ray Diffraction 1.755 1.8177 -- 141 2670 0.2376 0.2532 -- 99.0
X Ray Diffraction 1.8177 1.8904 -- 139 2648 0.217 0.2537 -- 100.0
X Ray Diffraction 1.8904 1.9764 -- 143 2710 0.213 0.2496 -- 99.0
X Ray Diffraction 1.9764 2.0806 -- 139 2640 0.1892 0.2358 -- 100.0
X Ray Diffraction 2.0806 2.2109 -- 140 2656 0.1912 0.2126 -- 100.0
X Ray Diffraction 2.2109 2.3815 -- 142 2696 0.1969 0.2571 -- 100.0
X Ray Diffraction 2.3815 2.621 -- 140 2664 0.1817 0.1845 -- 100.0
X Ray Diffraction 2.621 2.9998 -- 140 2661 0.1898 0.2009 -- 100.0
X Ray Diffraction 2.9998 3.7778 -- 142 2701 0.1903 0.2204 -- 100.0
X Ray Diffraction 3.7778 26.8292 -- 137 2629 0.2029 0.2143 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.3738
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3738
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7476
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.083
f_dihedral_angle_d 14.581
f_angle_d 1.495
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2076
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 77

Software

Computing
Computing Package Purpose
BlueIce Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: dev_986) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_986) refinement
AMoRE model building
BlueIce data collection