X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 293.0
Details 0.79M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.16 α = 90
b = 90.09 β = 90
c = 99.33 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 RIGAKU SATURN 944 -- 2010-01-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5419 -- --

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
1.9 42.07 98.3 -- -- -- -- -- 55684 1.0 1.0 --
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)
1.9 1.97 93.6 -- -- -- -- --

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 1.9 42.07 -- 0.0 -- 52372 2659 92.46 -- 0.193 0.1914 0.2224 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 1.9 1.9346 -- 108 2090 0.3633 0.4214 -- 75.0
X Ray Diffraction 1.9346 1.9718 -- 116 2260 0.3223 0.363 -- 81.0
X Ray Diffraction 1.9718 2.012 -- 123 2324 0.2671 0.3045 -- 84.0
X Ray Diffraction 2.012 2.0558 -- 129 2415 0.2375 0.2724 -- 86.0
X Ray Diffraction 2.0558 2.1036 -- 149 2487 0.2274 0.2523 -- 89.0
X Ray Diffraction 2.1036 2.1562 -- 141 2508 0.2096 0.2468 -- 90.0
X Ray Diffraction 2.1562 2.2145 -- 132 2564 0.211 0.2375 -- 91.0
X Ray Diffraction 2.2145 2.2797 -- 140 2636 0.2031 0.2671 -- 94.0
X Ray Diffraction 2.2797 2.3532 -- 122 2654 0.2065 0.2406 -- 94.0
X Ray Diffraction 2.3532 2.4373 -- 142 2623 0.2083 0.316 -- 94.0
X Ray Diffraction 2.4373 2.5349 -- 150 2619 0.1985 0.2313 -- 94.0
X Ray Diffraction 2.5349 2.6503 -- 123 2720 0.2096 0.2621 -- 95.0
X Ray Diffraction 2.6503 2.79 -- 162 2717 0.2022 0.2055 -- 97.0
X Ray Diffraction 2.79 2.9647 -- 130 2765 0.199 0.254 -- 97.0
X Ray Diffraction 2.9647 3.1936 -- 153 2798 0.1987 0.221 -- 98.0
X Ray Diffraction 3.1936 3.5148 -- 156 2827 0.1934 0.2498 -- 99.0
X Ray Diffraction 3.5148 4.023 -- 151 2842 0.1671 0.1785 -- 99.0
X Ray Diffraction 4.023 5.0672 -- 159 2868 0.1447 0.1715 -- 99.0
X Ray Diffraction 5.0672 42.0807 -- 173 2996 0.1816 0.1971 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.9733
Anisotropic B[1][1] -0.5476
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.176
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.7236
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.36
f_plane_restr 0.005
f_chiral_restr 0.06
f_angle_d 0.886
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3400
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 292

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CrystalClear data collection