X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 0.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 30% v/v (+/-)-2-methyl-2,4-pentanedio, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.9 α = 90
b = 63.9 β = 90
c = 365.92 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2012-06-15
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 3W1A 0.9793 BSRF 3W1A

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
2.4 50 100.0 0.082 -- -- 17.6 18525 18525 0.0 0.0 --
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)
2.4 2.44 94.3 0.433 -- 4.0 12.9 850

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 2.398 38.001 -- 1.34 -- 18525 950 98.66 0.1884 0.1884 0.1865 0.2256 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 2.3981 2.4686 -- 139 2352 0.3026 0.4039 -- 90.0
X Ray Diffraction 2.4686 2.5483 -- 139 2523 0.2392 0.3076 -- 98.0
X Ray Diffraction 2.5483 2.6393 -- 152 2531 0.2107 0.2729 -- 98.0
X Ray Diffraction 2.6393 2.745 -- 137 2533 0.1888 0.2241 -- 99.0
X Ray Diffraction 2.745 2.8699 -- 149 2590 0.1872 0.2271 -- 99.0
X Ray Diffraction 2.8699 3.0211 -- 145 2595 0.1927 0.2561 -- 100.0
X Ray Diffraction 3.0211 3.2103 -- 166 2560 0.1984 0.2968 -- 100.0
X Ray Diffraction 3.2103 3.458 -- 136 2574 0.1964 0.2931 -- 100.0
X Ray Diffraction 3.458 3.8057 -- 125 2593 0.1918 0.2223 -- 100.0
X Ray Diffraction 3.8057 4.3558 -- 132 2585 0.161 0.1717 -- 100.0
X Ray Diffraction 4.3558 5.4852 -- 125 2614 0.1403 0.1436 -- 100.0
X Ray Diffraction 5.4852 38.0062 -- 115 2624 0.1962 0.1943 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 6.7307
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.7307
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.4614
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.073
f_dihedral_angle_d 13.957
f_angle_d 1.064
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1997
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 114

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
SOLVE model building
MAR345dtb data collection