X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 291.0
Details 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.75 α = 90
b = 79.96 β = 107.52
c = 55.32 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 RIGAKU SATURN 92 mirrors 2012-08-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
1.85 50 97.3 0.053 0.053 -- 3.8 36019 35045 0.0 -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)
1.85 1.92 87.9 0.318 0.318 2.778 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 1.85 24.198 -- 0.0 -- 33042 3285 91.78 -- 0.1842 0.179 0.2312 RANDOM
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 1.85 1.8774 -- 93 960 0.2601 0.3389 -- 69.0
X Ray Diffraction 1.8774 1.9067 -- 117 1086 0.2353 0.3387 -- 75.0
X Ray Diffraction 1.9067 1.938 -- 116 1074 0.2173 0.2939 -- 78.0
X Ray Diffraction 1.938 1.9714 -- 142 1171 0.2133 0.303 -- 84.0
X Ray Diffraction 1.9714 2.0072 -- 132 1224 0.1883 0.2829 -- 88.0
X Ray Diffraction 2.0072 2.0458 -- 130 1287 0.2019 0.2855 -- 90.0
X Ray Diffraction 2.0458 2.0875 -- 145 1263 0.1899 0.2553 -- 91.0
X Ray Diffraction 2.0875 2.1329 -- 159 1321 0.1837 0.2456 -- 94.0
X Ray Diffraction 2.1329 2.1825 -- 145 1305 0.1911 0.2428 -- 95.0
X Ray Diffraction 2.1825 2.237 -- 159 1355 0.1894 0.2761 -- 96.0
X Ray Diffraction 2.237 2.2974 -- 151 1335 0.1821 0.2472 -- 94.0
X Ray Diffraction 2.2974 2.365 -- 154 1312 0.184 0.2275 -- 95.0
X Ray Diffraction 2.365 2.4413 -- 159 1330 0.1879 0.2628 -- 95.0
X Ray Diffraction 2.4413 2.5284 -- 144 1338 0.1955 0.2298 -- 94.0
X Ray Diffraction 2.5284 2.6295 -- 144 1355 0.2061 0.2698 -- 96.0
X Ray Diffraction 2.6295 2.7491 -- 145 1358 0.1993 0.2595 -- 96.0
X Ray Diffraction 2.7491 2.8938 -- 159 1335 0.1926 0.2379 -- 96.0
X Ray Diffraction 2.8938 3.0747 -- 147 1390 0.1983 0.2571 -- 97.0
X Ray Diffraction 3.0747 3.3116 -- 162 1373 0.1876 0.2132 -- 98.0
X Ray Diffraction 3.3116 3.6438 -- 137 1416 0.1793 0.2357 -- 99.0
X Ray Diffraction 3.6438 4.1688 -- 139 1368 0.1417 0.1997 -- 96.0
X Ray Diffraction 4.1688 5.2434 -- 148 1358 0.1374 0.1698 -- 95.0
X Ray Diffraction 5.2434 24.2 -- 158 1443 0.1733 0.2006 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.1664
Anisotropic B[1][1] 1.1109
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.5379
Anisotropic B[2][2] 0.3114
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.4223
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.907
f_plane_restr 0.005
f_chiral_restr 0.062
f_angle_d 1.124
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2612
Nucleic Acid Atoms 651
Heterogen Atoms 43
Solvent Atoms 407

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction