X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Combined with Microseeding
pH 6.5
Temperature 293.0
Details 30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.32 α = 90
b = 82.91 β = 106.08
c = 41.4 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 -- 2007-04-13
Diffraction Radiation
Monochromator Protocol
Custom SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID

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
1.48 31 99.1 0.042 -- -- 4.8 39281 39281 -3.0 -3.0 17.72
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)
1.48 1.49 91.3 0.045 -- 1.9 4.0 933

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 1.479 30.972 -- 1.37 39281 39277 1972 98.87 -- 0.173 0.1716 0.1994 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 1.4786 1.5155 2513 121 2392 0.2358 0.3062 -- 89.0
X Ray Diffraction 1.5155 1.5565 2736 139 2597 0.2095 0.25 -- 96.0
X Ray Diffraction 1.5565 1.6023 2839 147 2692 0.1913 0.2144 -- 99.0
X Ray Diffraction 1.6023 1.654 2826 133 2693 0.1802 0.2171 -- 100.0
X Ray Diffraction 1.654 1.7131 2820 127 2693 0.1688 0.2057 -- 100.0
X Ray Diffraction 1.7131 1.7817 2838 129 2709 0.1616 0.2133 -- 100.0
X Ray Diffraction 1.7817 1.8628 2804 137 2667 0.1639 0.2165 -- 100.0
X Ray Diffraction 1.8628 1.961 2850 166 2684 0.1573 0.1904 -- 100.0
X Ray Diffraction 1.961 2.0838 2818 150 2668 0.1549 0.1886 -- 100.0
X Ray Diffraction 2.0838 2.2447 2832 137 2695 0.1576 0.1818 -- 100.0
X Ray Diffraction 2.2447 2.4705 2830 134 2696 0.166 0.183 -- 100.0
X Ray Diffraction 2.4705 2.8278 2851 154 2697 0.1638 0.2013 -- 100.0
X Ray Diffraction 2.8278 3.5619 2853 151 2702 0.1626 0.1897 -- 100.0
X Ray Diffraction 3.5619 30.9787 2867 147 2720 0.1799 0.1936 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 24.4
Anisotropic B[1][1] 4.4438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.8903
Anisotropic B[2][2] -2.095
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.3488
RMS Deviations
Key Refinement Restraint Deviation
f_planarity_d 0.007
f_dihedral_angle_d 15.348
f_improper_angle_d 0.097
f_angle_deg 1.226
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1804
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 175

Software

Computing
Computing Package Purpose
Custom Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX 1.3 Structure Refinement
Software
Software Name Purpose
PHENIX version: 1.3 refinement
Phaser model building
Custom data collection