X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM acetyl-CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.61 α = 90
b = 110.56 β = 90
c = 119.46 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-07-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.0331 APS 23-ID-D

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
1.74 50 100.0 0.124 0.124 -- 9.5 91574 91574 -- -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)
1.75 1.81 100.0 0.623 0.623 3.6 7.3 9057

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 1.743 42.795 -- 0.0 -- 88314 4400 96.06 -- 0.1695 0.1674 0.2086 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 1.7432 1.8055 7847 398 7449 0.2176 0.2825 -- 86.0
X Ray Diffraction 1.8055 1.8778 8473 393 8080 0.1971 0.2579 -- 93.0
X Ray Diffraction 1.8778 1.9633 8532 424 8108 0.1803 0.24 -- 94.0
X Ray Diffraction 1.9633 2.0668 8707 437 8270 0.1711 0.2309 -- 96.0
X Ray Diffraction 2.0668 2.1963 8843 442 8401 0.1632 0.2121 -- 97.0
X Ray Diffraction 2.1963 2.3658 8947 470 8477 0.1753 0.2318 -- 98.0
X Ray Diffraction 2.3658 2.6039 9041 451 8590 0.1725 0.2137 -- 98.0
X Ray Diffraction 2.6039 2.9806 9100 453 8647 0.1749 0.2186 -- 99.0
X Ray Diffraction 2.9806 3.7549 9263 455 8808 0.159 0.1918 -- 100.0
X Ray Diffraction 3.7549 42.808 9561 477 9084 0.1468 0.1662 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.0268
Anisotropic B[1][1] 0.4232
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.0447
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.468
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.988
f_plane_restr 0.006
f_chiral_restr 0.07
f_angle_d 1.06
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7768
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 981

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