X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 27.36 α = 90
b = 39.31 β = 99.41
c = 30.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2012-10-22
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0, 0.91942, 0.92006 PHOTON FACTORY AR-NW12A

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
1.4 21.94 -- -- -- -- -- -- 12212 -- -- --

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
MAD 1.4 21.94 -- 0.0 -- 12212 1260 96.4 -- -- 0.2323 0.2662 --
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 1.4 1.45 -- 124 1132 0.4596 0.4495 -- 98.0
X Ray Diffraction 1.45 1.51 -- 109 1110 0.4439 0.4432 -- 98.0
X Ray Diffraction 1.51 1.58 -- 144 1071 0.3337 0.3553 -- 97.9
X Ray Diffraction 1.58 1.66 -- 119 1120 0.2934 0.4039 -- 98.7
X Ray Diffraction 1.66 1.76 -- 146 1111 0.2234 0.2983 -- 98.8
X Ray Diffraction 1.76 1.9 -- 112 1135 0.2309 0.2625 -- 99.0
X Ray Diffraction 1.9 2.09 -- 141 1051 0.2693 0.2955 -- 93.9
X Ray Diffraction 2.09 2.39 -- 107 999 0.2241 0.2965 -- 87.7
X Ray Diffraction 2.39 3.02 -- 140 1140 0.1991 0.2379 -- 99.3
X Ray Diffraction 3.02 100.0 -- 118 1083 0.1722 0.1865 -- 92.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.0444
Anisotropic B[1][1] -1.441
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 9.21
Anisotropic B[2][2] -3.437
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.878
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.986
c_mcbond_it 1.494
c_angle_deg 0.964
c_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 486
Heterogen Atoms 0
Solvent Atoms 135

Software

Computing
Computing Package Purpose
CrystalClear Data Reduction (intensity integration)
CrystalClear Data Reduction (data scaling)
Phenix Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
CNS refinement