X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.7
Temperature 294.0
Details 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.56 α = 90
b = 146.19 β = 90
c = 108.44 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-03-29
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C

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
2.9 50 99.1 0.134 -- -- 3.2 43151 42754 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)
2.9 3.0 99.3 0.765 -- -- 3.3 4226

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 2.9 49.565 -- 0.0 43201 42709 2154 98.9 0.2387 0.2387 0.2362 0.2855 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 2.9 2.9676 -- 137 2594 0.3099 0.3565 -- 96.0
X Ray Diffraction 2.9676 3.0418 -- 140 2697 0.3189 0.3563 -- 100.0
X Ray Diffraction 3.0418 3.124 -- 149 2658 0.3047 0.3783 -- 99.0
X Ray Diffraction 3.124 3.216 -- 140 2665 0.2936 0.3466 -- 99.0
X Ray Diffraction 3.216 3.3197 -- 145 2673 0.2802 0.3085 -- 99.0
X Ray Diffraction 3.3197 3.4384 -- 143 2661 0.2643 0.3148 -- 98.0
X Ray Diffraction 3.4384 3.576 -- 153 2674 0.2517 0.3084 -- 99.0
X Ray Diffraction 3.576 3.7387 -- 149 2678 0.2296 0.3136 -- 99.0
X Ray Diffraction 3.7387 3.9357 -- 146 2675 0.2311 0.2796 -- 99.0
X Ray Diffraction 3.9357 4.1822 -- 128 2744 0.2131 0.2409 -- 99.0
X Ray Diffraction 4.1822 4.5049 -- 152 2691 0.1997 0.2442 -- 98.0
X Ray Diffraction 4.5049 4.9579 -- 117 2738 0.1937 0.243 -- 99.0
X Ray Diffraction 4.9579 5.6744 -- 149 2744 0.2196 0.2536 -- 100.0
X Ray Diffraction 5.6744 7.1457 -- 145 2767 0.2723 0.3461 -- 99.0
X Ray Diffraction 7.1457 49.5722 -- 161 2896 0.2076 0.2481 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.6706
Anisotropic B[1][1] -27.8803
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.9421
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -30.4193
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.874
f_plane_restr 0.004
f_chiral_restr 0.063
f_angle_d 0.842
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11406
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: dev_1000) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction