X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 25% PEG 2000 MME, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.56 α = 90
b = 70.56 β = 90
c = 506.3 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-10-03
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 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
3.1 50 82.0 -- -- -- -- 42807 42807 0.0 -3.0 57.19
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)
3.1 3.21 83.3 -- -- -- -- --

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 3.1 49.49 -- 1.99 42793 42793 2162 80.84 0.2481 0.2481 0.245 0.3069 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 3.0646 3.1359 -- 108 2193 0.3115 0.3935 -- 67.0
X Ray Diffraction 3.1359 3.2143 -- 139 2858 0.2812 0.3807 -- 82.0
X Ray Diffraction 3.2143 3.3012 -- 151 2755 0.2808 0.351 -- 85.0
X Ray Diffraction 3.3012 3.3983 -- 146 2798 0.2724 0.2945 -- 83.0
X Ray Diffraction 3.3983 3.5079 -- 166 2774 0.2901 0.3907 -- 83.0
X Ray Diffraction 3.5079 3.6333 -- 165 2694 0.268 0.3291 -- 82.0
X Ray Diffraction 3.6333 3.7787 -- 158 2715 0.2677 0.3237 -- 82.0
X Ray Diffraction 3.7787 3.9506 -- 153 2761 0.2543 0.3089 -- 81.0
X Ray Diffraction 3.9506 4.1588 -- 126 2709 0.2548 0.2788 -- 80.0
X Ray Diffraction 4.1588 4.4192 -- 151 2672 0.2343 0.3163 -- 80.0
X Ray Diffraction 4.4192 4.7602 -- 147 2668 0.2274 0.3476 -- 81.0
X Ray Diffraction 4.7602 5.2387 -- 114 2710 0.224 0.2702 -- 80.0
X Ray Diffraction 5.2387 5.9957 -- 146 2681 0.2295 0.3112 -- 80.0
X Ray Diffraction 5.9957 7.5496 -- 142 2695 0.2325 0.2548 -- 80.0
X Ray Diffraction 7.5496 49.4965 -- 150 2948 0.2064 0.2415 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.4869
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_angle_d 1.082
f_chiral_restr 0.126
f_dihedral_angle_d 17.546
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15476
Nucleic Acid Atoms 0
Heterogen Atoms 198
Solvent Atoms 0

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
HKL-2000 data reduction
HKL-2000 data scaling