X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 298.0
Details PEG8000, pH 7.8, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.46 α = 90
b = 76.25 β = 90
c = 81.38 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 225 mm CCD Rosenbaum-Rock vertical focusing mirror. 2012-10-10
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.56 50 99.3 0.11 -- -- 11.2 -- 59125 -- -- --
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)
1.56 1.59 90.2 0.487 -- -- 4.2 2652

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 1.6 33.069 -- 0.1 -- 52766 1897 95.54 -- 0.1604 0.1595 0.1841 --
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 1.6 1.64 -- 130 3330 0.2145 0.2577 -- 89.0
X Ray Diffraction 1.64 1.6844 -- 125 3421 0.1877 0.2254 -- 91.0
X Ray Diffraction 1.6844 1.7339 -- 129 3494 0.1679 0.2194 -- 93.0
X Ray Diffraction 1.7339 1.7899 -- 132 3568 0.1696 0.21 -- 95.0
X Ray Diffraction 1.7899 1.8538 -- 137 3572 0.1545 0.2009 -- 94.0
X Ray Diffraction 1.8538 1.9281 -- 132 3577 0.1542 0.175 -- 95.0
X Ray Diffraction 1.9281 2.0158 -- 133 3636 0.1603 0.1695 -- 96.0
X Ray Diffraction 2.0158 2.1221 -- 134 3632 0.1577 0.1963 -- 97.0
X Ray Diffraction 2.1221 2.255 -- 136 3722 0.1598 0.1947 -- 97.0
X Ray Diffraction 2.255 2.429 -- 138 3653 0.1597 0.1726 -- 97.0
X Ray Diffraction 2.429 2.6734 -- 136 3686 0.1622 0.1806 -- 97.0
X Ray Diffraction 2.6734 3.06 -- 137 3730 0.1682 0.219 -- 97.0
X Ray Diffraction 3.06 3.8543 -- 147 3845 0.1448 0.1671 -- 99.0
X Ray Diffraction 3.8543 33.0759 -- 151 4003 0.1523 0.15 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.2644
Anisotropic B[1][1] 1.6862
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.9105
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7758
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.27
f_plane_restr 0.006
f_chiral_restr 0.08
f_angle_d 1.556
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3459
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 538

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
HKL data reduction