X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 10% PEG3000, 100mM imidazole, 200mM lithium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.95 α = 90
b = 100.95 β = 90
c = 99.86 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-08-10
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U

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
2.5 50 100.0 0.112 -- -- 6.3 39254 39254 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)
2.5 2.54 95.1 0.61 -- 2.37 5.3 1887

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 2.5 35.497 -- 1.96 39254 38813 1948 98.57 -- 0.2241 0.2241 0.2797 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 2.5 2.5626 -- 137 2417 0.3729 0.4476 -- 91.0
X Ray Diffraction 2.5626 2.6319 -- 124 2571 0.3673 0.445 -- 96.0
X Ray Diffraction 2.6319 2.7093 -- 124 2662 0.3602 0.4557 -- 99.0
X Ray Diffraction 2.7093 2.7967 -- 145 2675 0.3177 0.3871 -- 100.0
X Ray Diffraction 2.7967 2.8966 -- 122 2671 0.3163 0.3616 -- 100.0
X Ray Diffraction 2.8966 3.0125 -- 147 2639 0.2956 0.3902 -- 100.0
X Ray Diffraction 3.0125 3.1496 -- 136 2678 0.2623 0.3656 -- 100.0
X Ray Diffraction 3.1496 3.3155 -- 130 2639 0.2315 0.2862 -- 98.0
X Ray Diffraction 3.3155 3.5231 -- 146 2654 0.2194 0.2797 -- 100.0
X Ray Diffraction 3.5231 3.7948 -- 123 2664 0.2463 0.3061 -- 99.0
X Ray Diffraction 3.7948 4.1761 -- 169 2643 0.1937 0.2498 -- 99.0
X Ray Diffraction 4.1761 4.7792 -- 138 2655 0.1712 0.2228 -- 100.0
X Ray Diffraction 4.7792 6.0165 -- 163 2637 0.1962 0.2675 -- 100.0
X Ray Diffraction 6.0165 35.5005 -- 144 2660 0.1766 0.2066 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -12.1068
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.1068
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 24.2137
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.083
f_dihedral_angle_d 21.655
f_angle_d 1.317
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5506
Nucleic Acid Atoms 1271
Heterogen Atoms 0
Solvent Atoms 65

Software

Computing
Computing Package Purpose
bluice 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
bluice data collection