X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 291.0
Details 20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.04 α = 90
b = 92.42 β = 90
c = 116.73 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 -- 2009-01-22
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 1.1159 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
2.48 50 100.0 0.054 -- -- 7.8 33390 33390 0.0 0.0 51.9
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)
2.48 2.57 100.0 0.642 -- 3.6 8.0 3277

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 2.48 43.022 -- 1.34 -- 33330 1630 99.7 -- 0.2402 0.2391 0.2594 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 2.48 2.5592 2650 128 2522 0.321 0.4057 -- 97.0
X Ray Diffraction 2.5592 2.6418 2749 132 2617 0.3245 0.3721 -- 100.0
X Ray Diffraction 2.6418 2.7362 2747 135 2612 0.3094 0.3671 -- 100.0
X Ray Diffraction 2.7362 2.8457 2741 132 2609 0.3084 0.3653 -- 100.0
X Ray Diffraction 2.8457 2.9752 2765 137 2628 0.2999 0.3935 -- 100.0
X Ray Diffraction 2.9752 3.132 2751 117 2634 0.3019 0.3343 -- 100.0
X Ray Diffraction 3.132 3.3282 2760 140 2620 0.2787 0.3086 -- 100.0
X Ray Diffraction 3.3282 3.585 2789 146 2643 0.2591 0.2552 -- 100.0
X Ray Diffraction 3.585 3.9456 2755 147 2608 0.2186 0.2143 -- 100.0
X Ray Diffraction 3.9456 4.516 2823 145 2678 0.1818 0.2226 -- 100.0
X Ray Diffraction 4.516 5.6876 2825 129 2696 0.1934 0.1809 -- 100.0
X Ray Diffraction 5.6876 43.0289 2975 142 2833 0.2014 0.212 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.96
Anisotropic B[1][1] -5.779
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.5679
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.3469
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.097
f_dihedral_angle_d 19.282
f_angle_d 1.216
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5941
Nucleic Acid Atoms 1039
Heterogen Atoms 20
Solvent Atoms 113

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