X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 20 mM magnesium acetate, 0.1 M MES, 12% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.01 α = 90
b = 299.51 β = 113.24
c = 145.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M-F -- 2011-11-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA

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
2.9 15 98.6 0.068 -- -- 3.5 236839 233547 2.0 2.0 --
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)
2.9 3.0 99.5 0.483 -- 3.91 -- --

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 2.9 15.0 -- -- 221869 221869 11678 98.74 -- 0.222 0.22158 0.22997 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 2.9 2.972 -- 830 15756 0.341 0.351 -- 99.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 74.888
Anisotropic B[1][1] 3.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.03
Anisotropic B[2][2] -8.83
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.45
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.003
r_chiral_restr 0.053
r_dihedral_angle_4_deg 10.362
r_dihedral_angle_3_deg 13.255
r_dihedral_angle_2_deg 35.176
r_dihedral_angle_1_deg 3.939
r_angle_refined_deg 0.836
r_bond_refined_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49538
Nucleic Acid Atoms 0
Heterogen Atoms 160
Solvent Atoms 1335

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
REFMAC Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
REFMAC model building
XDS data collection