X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.9 α = 90
b = 83.04 β = 108.54
c = 58.19 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 MAR scanner 300 mm plate -- 2010-12-18
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B

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
1.93 50 95.24 -- 0.05 -- 3.6 36045 36045 1.0 1.0 30.81
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)
1.93 1.96 74.65 -- 0.287 4.32 3.0 --

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 1.932 40.419 -- 0.0 34550 34548 1905 91.36 -- 0.1747 0.1727 0.2086 --
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 1.932 1.9803 -- 82 1581 0.2174 0.2953 -- 63.0
X Ray Diffraction 1.9803 2.0338 -- 119 1918 0.2185 0.2626 -- 76.0
X Ray Diffraction 2.0338 2.0937 -- 117 2046 0.2006 0.237 -- 80.0
X Ray Diffraction 2.0937 2.1612 -- 126 2248 0.195 0.248 -- 88.0
X Ray Diffraction 2.1612 2.2385 -- 131 2329 0.1947 0.2287 -- 92.0
X Ray Diffraction 2.2385 2.3281 -- 154 2414 0.1796 0.2505 -- 95.0
X Ray Diffraction 2.3281 2.434 -- 139 2479 0.1786 0.2314 -- 97.0
X Ray Diffraction 2.434 2.5624 -- 142 2477 0.1791 0.2575 -- 98.0
X Ray Diffraction 2.5624 2.7229 -- 151 2499 0.1834 0.222 -- 98.0
X Ray Diffraction 2.7229 2.933 -- 150 2522 0.1841 0.2561 -- 99.0
X Ray Diffraction 2.933 3.2281 -- 144 2524 0.183 0.2157 -- 99.0
X Ray Diffraction 3.2281 3.6949 -- 146 2521 0.1676 0.2134 -- 99.0
X Ray Diffraction 3.6949 4.6541 -- 155 2542 0.141 0.1714 -- 99.0
X Ray Diffraction 4.6541 40.419 -- 149 2543 0.1727 0.172 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -8.0369
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 6.9423
Anisotropic B[2][2] 16.4824
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.4455
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.062
f_dihedral_angle_d 14.609
f_angle_d 1.063
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3831
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 243

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr) Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.automr) model building
HKL-2000 data collection