X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 291.0
Details 80mM NaCl, 12mM KCl, 20mM MgCl2, 40mM sodium cacodylate, 12mM spermine, 28% 2-methyl-1,3 propanediol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.46 α = 90
b = 41.51 β = 106.76
c = 90.42 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 210 -- 2012-07-01
Diffraction Radiation
Monochromator Protocol
Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.9767 CHESS A1

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
2.65 35 97.2 0.068 -- -- 3.6 -- 11578 -- -3.0 48.89
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)
2.65 2.7 82.7 0.484 -- 1.808 3.1 473

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
SAD 2.673 20.14 -- 1.35 -- 11484 1151 95.71 -- 0.2051 0.201 0.2427 --
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 2.6732 2.7945 -- 118 1054 0.3358 0.3642 -- 79.0
X Ray Diffraction 2.7945 2.9414 -- 139 1257 0.322 0.3948 -- 93.0
X Ray Diffraction 2.9414 3.1251 -- 145 1304 0.2628 0.3302 -- 99.0
X Ray Diffraction 3.1251 3.3654 -- 144 1304 0.2216 0.2522 -- 98.0
X Ray Diffraction 3.3654 3.7022 -- 148 1310 0.1883 0.2475 -- 97.0
X Ray Diffraction 3.7022 4.2335 -- 151 1347 0.1636 0.2074 -- 100.0
X Ray Diffraction 4.2335 5.3175 -- 151 1364 0.1738 0.2261 -- 100.0
X Ray Diffraction 5.3175 20.1403 -- 155 1393 0.1767 0.1969 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.9439
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.385
f_plane_restr 0.002
f_chiral_restr 0.019
f_angle_d 0.409
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 2472
Heterogen Atoms 2
Solvent Atoms 25

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE version: 2.15 density modification
SOLVE phasing
SCALEPACK data reduction
DENZO data collection