X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 297.0
Details 100mM imidazole, 35% 2-methyl-2,4-pentanediol, 200mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.29 α = 90
b = 178.56 β = 102.97
c = 109.23 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2005-04-06
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0629 PAL/PLS 4A

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
2.61 50 100.0 0.08 -- -- -- 420103 66140 -- -- --
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)
2.61 2.7 100.0 0.373 -- -- -- --

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 2.7 19.978 -- 0.0 -- 58910 3007 97.43 -- 0.1768 0.1731 0.2456 --
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 2.7 2.7442 -- 143 2473 0.2378 0.3246 -- 92.0
X Ray Diffraction 2.7442 2.7914 -- 132 2529 0.238 0.3307 -- 92.0
X Ray Diffraction 2.7914 2.842 -- 149 2552 0.2449 0.3635 -- 94.0
X Ray Diffraction 2.842 2.8965 -- 162 2528 0.2179 0.3133 -- 94.0
X Ray Diffraction 2.8965 2.9554 -- 132 2652 0.2008 0.2665 -- 96.0
X Ray Diffraction 2.9554 3.0195 -- 130 2598 0.2023 0.308 -- 96.0
X Ray Diffraction 3.0195 3.0895 -- 121 2661 0.2016 0.3076 -- 97.0
X Ray Diffraction 3.0895 3.1664 -- 153 2605 0.1972 0.2767 -- 97.0
X Ray Diffraction 3.1664 3.2517 -- 149 2649 0.2006 0.2736 -- 97.0
X Ray Diffraction 3.2517 3.3469 -- 153 2677 0.1851 0.2739 -- 98.0
X Ray Diffraction 3.3469 3.4544 -- 142 2711 0.1769 0.2489 -- 98.0
X Ray Diffraction 3.4544 3.5772 -- 134 2686 0.1742 0.2499 -- 99.0
X Ray Diffraction 3.5772 3.7196 -- 135 2765 0.1833 0.2634 -- 100.0
X Ray Diffraction 3.7196 3.8877 -- 150 2682 0.1668 0.2344 -- 99.0
X Ray Diffraction 3.8877 4.091 -- 148 2694 0.1544 0.2294 -- 99.0
X Ray Diffraction 4.091 4.3449 -- 141 2721 0.1447 0.2219 -- 99.0
X Ray Diffraction 4.3449 4.6763 -- 157 2722 0.1379 0.1856 -- 100.0
X Ray Diffraction 4.6763 5.1397 -- 147 2705 0.1538 0.223 -- 100.0
X Ray Diffraction 5.1397 5.8669 -- 145 2782 0.193 0.2666 -- 100.0
X Ray Diffraction 5.8669 7.3304 -- 151 2722 0.1925 0.2619 -- 100.0
X Ray Diffraction 7.3304 19.9782 -- 133 2789 0.1348 0.1768 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 4.9375
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.4692
Anisotropic B[2][2] -9.1603
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.2228
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 16.448
f_angle_d 1.185
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14784
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 344

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
CNS model building
HKL-2000 data collection