X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.74
Temperature 298.0
Details 20% PEG 4000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, 2% benzamidine hydrochloride, pH 6.74, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.57 α = 90
b = 59.57 β = 90
c = 291.18 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-03-18
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.20610, 1.25494, 1.25525 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
2.96 50 94.4 0.081 -- -- 12.5 -- 11205 -- -- --
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)
2.96 3.08 63.2 0.26 -- -- 7.7 705

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
MAD 2.96 46.099 -- 0.12 -- 10606 1060 89.44 -- 0.2189 0.2135 0.2662 --
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 2.96 3.0896 -- 75 677 0.3144 0.491 -- 53.0
X Ray Diffraction 3.0896 3.2525 -- 116 1014 0.2638 0.3512 -- 78.0
X Ray Diffraction 3.2525 3.4562 -- 128 1194 0.2159 0.2895 -- 92.0
X Ray Diffraction 3.4562 3.7229 -- 144 1257 0.2276 0.2986 -- 95.0
X Ray Diffraction 3.7229 4.0974 -- 139 1268 0.2094 0.2688 -- 98.0
X Ray Diffraction 4.0974 4.6898 -- 149 1322 0.185 0.232 -- 98.0
X Ray Diffraction 4.6898 5.9067 -- 149 1340 0.1948 0.2571 -- 99.0
X Ray Diffraction 5.9067 46.1049 -- 160 1474 0.1971 0.2216 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.2251
Anisotropic B[1][1] 13.9864
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 13.9864
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -27.9729
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 22.281
f_plane_restr 0.004
f_chiral_restr 0.064
f_angle_d 1.354
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2249
Nucleic Acid Atoms 937
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
JBluIce-EPICS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
RESOLVE version: 2.13 density modification
SOLVE phasing
HKL data processing