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_plane_restr 0.005
f_angle_d 1.124
f_chiral_restr 0.062
f_bond_d 0.017
f_dihedral_angle_d 18.907
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

Software
Software Name Purpose
HKL data reduction
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.11
StructureStudio data collection
HKL data scaling