X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.06 α = 90
b = 91.85 β = 90
c = 115.94 γ = 90
Symmetry
Space Group P 21 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-10-18
Diffraction Radiation
Monochromator Protocol
DOUBLE FLAT CRYSTAL, SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.2823 ALS 8.3.1

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
2.98 50 91.4 0.102 -- -- 4.3 19750 18071 0.0 0.0 72.6
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)
2.98 3.07 94.0 0.538 -- 2.1 4.4 1827

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 2.98 49.023 -- 1.9 -- 17619 1549 86.23 -- 0.2408 0.2391 0.2733 IMPORTED FROM PDB ENTRY 3L4J
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 2.98 3.0795 2849 127 2722 0.3373 0.3943 -- 86.0
X Ray Diffraction 3.0795 3.1895 2869 129 2740 0.3301 0.365 -- 88.0
X Ray Diffraction 3.1895 3.3172 2863 153 2710 0.3276 0.398 -- 88.0
X Ray Diffraction 3.3172 3.4682 2876 171 2705 0.299 0.3261 -- 87.0
X Ray Diffraction 3.4682 3.651 2849 143 2706 0.2725 0.347 -- 87.0
X Ray Diffraction 3.651 3.8796 2873 157 2716 0.2549 0.2904 -- 87.0
X Ray Diffraction 3.8796 4.179 2824 137 2687 0.2291 0.2826 -- 86.0
X Ray Diffraction 4.179 4.5993 2799 139 2660 0.1971 0.2457 -- 85.0
X Ray Diffraction 4.5993 5.2641 2791 132 2659 0.1961 0.1875 -- 85.0
X Ray Diffraction 5.2641 6.6297 2796 113 2683 0.213 0.2677 -- 85.0
X Ray Diffraction 6.6297 49.0292 2791 148 2643 0.1935 0.209 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 89.9
Anisotropic B[1][1] -8.8659
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.0089
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.143
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.103
f_dihedral_angle_d 18.072
f_angle_d 1.25
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5941
Nucleic Acid Atoms 1039
Heterogen Atoms 28
Solvent Atoms 20

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.5_2) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.5_2) refinement
PHASER model building
BLU-ICE data collection