X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 20% PEG3350, 5% iso-propanol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.44 α = 90
b = 109.74 β = 90
c = 130.68 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 MAR scanner 300 mm plate -- 2008-06-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-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
2.5 49.4 89.7 0.134 0.155 -- 4.6 27379 24559 0.0 0.0 56.8
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)
2.5 2.54 62.9 0.497 0.46 2.2 1.8 --

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 2.5 49.4 -- 1.42 27496 24129 1970 87.79 -- 0.2333 0.2284 0.2887 --
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 2.4966 2.5591 -- 90 1009 0.3274 0.4201 -- 56.0
X Ray Diffraction 2.5591 2.6283 -- 100 1163 0.3145 0.4125 -- 66.0
X Ray Diffraction 2.6283 2.7056 -- 113 1264 0.3217 0.3581 -- 72.0
X Ray Diffraction 2.7056 2.7929 -- 122 1363 0.3084 0.4188 -- 76.0
X Ray Diffraction 2.7929 2.8927 -- 133 1482 0.306 0.4086 -- 84.0
X Ray Diffraction 2.8927 3.0085 -- 141 1576 0.2947 0.4087 -- 88.0
X Ray Diffraction 3.0085 3.1454 -- 151 1691 0.2928 0.3515 -- 94.0
X Ray Diffraction 3.1454 3.3112 -- 153 1721 0.2634 0.3036 -- 97.0
X Ray Diffraction 3.3112 3.5186 -- 156 1758 0.2444 0.3366 -- 99.0
X Ray Diffraction 3.5186 3.7902 -- 159 1793 0.2337 0.2584 -- 99.0
X Ray Diffraction 3.7902 4.1715 -- 160 1793 0.2098 0.2926 -- 99.0
X Ray Diffraction 4.1715 4.7747 -- 159 1803 0.1835 0.2302 -- 99.0
X Ray Diffraction 4.7747 6.0139 -- 164 1833 0.1957 0.2446 -- 99.0
X Ray Diffraction 6.0139 49.4776 -- 169 1910 0.2117 0.2651 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.8165
Anisotropic B[1][1] 2.8745
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3003
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.5742
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.022
f_dihedral_angle_d 7.027
f_angle_d 0.359
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5533
Nucleic Acid Atoms 0
Heterogen Atoms 121
Solvent Atoms 113

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement