X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 2 M ammonium sulfate, 0.1 M sodium cacodylate, 0.2 M sodium chloride, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 150.18 α = 90
b = 150.18 β = 90
c = 290.39 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-10-09
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G

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
2.8 50 97.1 0.114 0.114 -- 18.0 46836 46836 -- -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)
2.8 2.85 92.2 0.718 0.718 3.9 12.5 2173

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 2.802 41.541 -- 0.0 -- 44896 2273 92.99 -- 0.1801 0.1779 0.2231 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 2.802 2.9021 3823 201 3622 0.2866 0.3592 -- 81.0
X Ray Diffraction 2.9021 3.0183 4145 214 3931 0.2512 0.3135 -- 87.0
X Ray Diffraction 3.0183 3.1556 4234 211 4023 0.2553 0.3179 -- 89.0
X Ray Diffraction 3.1556 3.3219 4319 221 4098 0.2271 0.3086 -- 91.0
X Ray Diffraction 3.3219 3.53 4376 220 4156 0.2001 0.2399 -- 92.0
X Ray Diffraction 3.53 3.8023 4501 230 4271 0.1732 0.2154 -- 94.0
X Ray Diffraction 3.8023 4.1847 4723 237 4486 0.1575 0.2061 -- 98.0
X Ray Diffraction 4.1847 4.7894 4814 241 4573 0.1326 0.1742 -- 99.0
X Ray Diffraction 4.7894 6.0312 4908 247 4661 0.1533 0.1924 -- 100.0
X Ray Diffraction 6.0312 41.5456 5053 251 4802 0.1601 0.183 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.7383
Anisotropic B[1][1] 2.1712
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.1712
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.3423
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.606
f_plane_restr 0.006
f_chiral_restr 0.072
f_angle_d 1.201
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7684
Nucleic Acid Atoms 0
Heterogen Atoms 200
Solvent Atoms 295

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.3_473) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction