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 = 55.86 α = 90
b = 83.5 β = 108.54
c = 58.61 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
2.24 50 95.13 -- 0.089 -- 3.1 23428 23428 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)
2.24 2.28 75.6 -- 0.239 4.57 2.1 --

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 2.24 46.411 -- 0.0 22209 22209 1907 90.18 -- 0.1887 0.1851 0.2267 --
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 2.24 2.2962 -- 92 1007 0.2224 0.2826 -- 64.0
X Ray Diffraction 2.2962 2.3583 -- 121 1202 0.2216 0.282 -- 75.0
X Ray Diffraction 2.3583 2.4277 -- 117 1355 0.2044 0.31 -- 83.0
X Ray Diffraction 2.4277 2.506 -- 130 1347 0.1873 0.208 -- 86.0
X Ray Diffraction 2.506 2.5956 -- 133 1415 0.2014 0.2617 -- 89.0
X Ray Diffraction 2.5956 2.6995 -- 134 1456 0.1962 0.2665 -- 91.0
X Ray Diffraction 2.6995 2.8223 -- 139 1497 0.2065 0.2199 -- 93.0
X Ray Diffraction 2.8223 2.9711 -- 141 1535 0.2006 0.2501 -- 95.0
X Ray Diffraction 2.9711 3.1572 -- 140 1525 0.1926 0.2553 -- 96.0
X Ray Diffraction 3.1572 3.4009 -- 152 1557 0.1929 0.2062 -- 97.0
X Ray Diffraction 3.4009 3.743 -- 146 1594 0.172 0.2215 -- 98.0
X Ray Diffraction 3.743 4.2843 -- 155 1580 0.1573 0.186 -- 99.0
X Ray Diffraction 4.2843 5.3965 -- 151 1604 0.157 0.1911 -- 99.0
X Ray Diffraction 5.3965 46.4211 -- 156 1628 0.1994 0.2426 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.0533
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.371
Anisotropic B[2][2] 8.5425
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.4891
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.052
f_dihedral_angle_d 16.016
f_angle_d 1.272
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3911
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 178

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: 1.7.1_743) 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