X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.3
Temperature 295.0
Details 0.1M MgCl2, 0.1M Sodium Acetate, 30% PEG400, 8%(v/v)1,3-Butanediol, pH 4.3, VAPOR DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.14 α = 90
b = 163.4 β = 90
c = 39.67 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-12-12
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.54001 SSRF BL17U

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
2.43 40.85 96.6 0.049 0.049 -- 4.95 13931 13895 -3.0 -3.0 46.6
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)
2.43 2.58 95.8 -- 0.254 4.77 3.97 2174

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 2.431 40.85 -- 1.88 13893 13893 694 96.31 -- 0.2647 0.264 0.2797 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 2.4314 2.6191 -- 136 2583 0.3532 0.3778 -- 97.0
X Ray Diffraction 2.6191 2.8826 -- 142 2686 0.3181 0.3579 -- 100.0
X Ray Diffraction 2.8826 3.2995 -- 140 2695 0.291 0.2874 -- 99.0
X Ray Diffraction 3.2995 4.1564 -- 125 2367 0.2843 0.2935 -- 87.0
X Ray Diffraction 4.1564 40.8557 -- 151 2868 0.2058 0.2245 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.666
Anisotropic B[1][1] 11.0965
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.1143
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.9822
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 25.488
f_plane_restr 0.003
f_chiral_restr 0.036
f_angle_d 0.748
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 931
Nucleic Acid Atoms 1060
Heterogen Atoms 0
Solvent Atoms 70

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS package Data Reduction (intensity integration)
XDS package Data Reduction (data scaling)
Phaser for MR Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
Phaser version: for MR model building
ADSC version: Quantum data collection