X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 15% PEG200, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.15 α = 90
b = 333.18 β = 90
c = 58.49 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-12-04
Diffraction Radiation
Monochromator Protocol
Si 111 Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA

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
2.79 48.06 100.0 0.105 -- -- -- 43217 43203 -3.0 -3.0 --
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)
2.79 2.87 100.0 0.549 -- 5.01 -- --

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 2.79 48.058 -- 2.02 43217 43194 2188 98.65 -- 0.161 0.1584 0.2082 --
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 2.79 2.8854 -- 185 3506 0.2179 0.2927 -- 86.0
X Ray Diffraction 2.8854 3.0009 -- 212 4092 0.1737 0.2214 -- 100.0
X Ray Diffraction 3.0009 3.1375 -- 210 4075 0.1641 0.241 -- 100.0
X Ray Diffraction 3.1375 3.3029 -- 218 4118 0.1566 0.2262 -- 100.0
X Ray Diffraction 3.3029 3.5098 -- 227 4115 0.1551 0.2409 -- 100.0
X Ray Diffraction 3.5098 3.7806 -- 222 4116 0.1466 0.1895 -- 100.0
X Ray Diffraction 3.7806 4.1609 -- 229 4166 0.1429 0.1915 -- 100.0
X Ray Diffraction 4.1609 4.7625 -- 230 4152 0.1259 0.1824 -- 100.0
X Ray Diffraction 4.7625 5.9985 -- 222 4209 0.1453 0.1788 -- 100.0
X Ray Diffraction 5.9985 48.0653 -- 233 4457 0.202 0.2315 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 4.8358
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.6892
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 16.6881
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 17.097
f_angle_d 1.149
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6648
Nucleic Acid Atoms 0
Heterogen Atoms 107
Solvent Atoms 429

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data reduction