X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 293.0
Details 65 mM KPi/22% PEG8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.6 α = 90
b = 77.04 β = 90
c = 86.85 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 -- 2011-10-16
Diffraction Radiation
Monochromator Protocol
Sagittally-focused Si(111) 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
2.4 20 85.9 0.085 -- -- 3.3 -- 23255 2.0 2.0 --
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)
2.5 2.59 41.3 0.352 -- -- 1.7 --

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 2.4 20.0 -- 0.19 15378 17495 1505 95.56 -- 0.1782 0.1726 0.2375 --
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 2.4 2.4775 -- 117 1239 0.1958 0.2932 -- 84.0
X Ray Diffraction 2.4775 2.566 -- 125 1336 0.1918 0.2687 -- 89.0
X Ray Diffraction 2.566 2.6688 -- 130 1376 0.1817 0.3121 -- 93.0
X Ray Diffraction 2.6688 2.7902 -- 134 1429 0.1882 0.2857 -- 96.0
X Ray Diffraction 2.7902 2.9373 -- 139 1467 0.1809 0.2811 -- 97.0
X Ray Diffraction 2.9373 3.1213 -- 140 1487 0.1929 0.2568 -- 98.0
X Ray Diffraction 3.1213 3.3622 -- 139 1490 0.1773 0.2489 -- 99.0
X Ray Diffraction 3.3622 3.7004 -- 141 1486 0.1659 0.2367 -- 98.0
X Ray Diffraction 3.7004 4.2354 -- 142 1517 0.152 0.1905 -- 98.0
X Ray Diffraction 4.2354 5.3347 -- 144 1534 0.1488 0.1857 -- 99.0
X Ray Diffraction 5.3347 43.8653 -- 154 1629 0.1858 0.2373 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 14.4948
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.927
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.5678
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 15.285
f_angle_d 1.316
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3652
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 117

Software

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