X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 0.2 M calcium chloride, 0.1 M HEPES, pH 6.8, 16% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.39 α = 90
b = 106.15 β = 90
c = 151.02 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-11-17
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) 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
2.7 50 99.8 0.161 0.161 -- 6.7 42837 42751 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)
2.7 2.8 99.8 0.69 0.69 2.4 6.6 --

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 2.712 48.697 0.0 1.36 44707 42563 2144 98.75 -- 0.2045 0.2018 0.2557 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 2.712 2.775 -- 101 2357 0.2499 0.2946 -- 88.0
X Ray Diffraction 2.775 2.8444 -- 158 2648 0.2709 0.3181 -- 100.0
X Ray Diffraction 2.8444 2.9213 -- 134 2691 0.2732 0.35 -- 100.0
X Ray Diffraction 2.9213 3.0073 -- 146 2685 0.2569 0.3658 -- 100.0
X Ray Diffraction 3.0073 3.1043 -- 136 2693 0.2487 0.3232 -- 100.0
X Ray Diffraction 3.1043 3.2152 -- 133 2722 0.2396 0.3012 -- 100.0
X Ray Diffraction 3.2152 3.3439 -- 153 2675 0.2223 0.2957 -- 100.0
X Ray Diffraction 3.3439 3.4961 -- 136 2709 0.2036 0.2929 -- 100.0
X Ray Diffraction 3.4961 3.6804 -- 155 2703 0.1859 0.2711 -- 100.0
X Ray Diffraction 3.6804 3.9108 -- 165 2709 0.1712 0.2071 -- 100.0
X Ray Diffraction 3.9108 4.2127 -- 142 2736 0.1615 0.1896 -- 100.0
X Ray Diffraction 4.2127 4.6363 -- 145 2751 0.1462 0.1893 -- 100.0
X Ray Diffraction 4.6363 5.3065 -- 138 2748 0.1556 0.2176 -- 100.0
X Ray Diffraction 5.3065 6.6828 -- 145 2787 0.2299 0.2781 -- 100.0
X Ray Diffraction 6.6828 48.7048 -- 157 2805 0.2014 0.2149 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 12.6433
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.4992
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.144
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.919
f_chiral_restr 0.065
f_bond_d 0.005
f_dihedral_angle_d 16.92
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10736
Nucleic Acid Atoms 0
Heterogen Atoms 108
Solvent Atoms 194

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.7.3_928)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing