X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 293.0
Details 24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.61 α = 90
b = 37.46 β = 90
c = 90.4 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Radiation
Monochromator Protocol
-- Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
Synchrotron ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4

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
1.35 26.18 99.3 -- -- -- -- 27862 27862 2.8 2.8 --
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)
1.35 1.42 99.9 0.559 -- 2.8 3.5 4013

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
SAD 1.35 23.266 -- 1.34 -- 27807 1361 99.02 -- 0.1562 0.1546 0.1891 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 1.35 1.3983 -- 115 2645 0.1992 0.2328 -- 100.0
X Ray Diffraction 1.3983 1.4542 -- 134 2617 0.1859 0.2579 -- 100.0
X Ray Diffraction 1.4542 1.5204 -- 132 2614 0.1686 0.222 -- 100.0
X Ray Diffraction 1.5204 1.6005 -- 128 2637 0.138 0.1952 -- 100.0
X Ray Diffraction 1.6005 1.7008 -- 140 2637 0.1266 0.1741 -- 100.0
X Ray Diffraction 1.7008 1.8321 -- 143 2644 0.116 0.1583 -- 100.0
X Ray Diffraction 1.8321 2.0163 -- 186 2610 0.1293 0.1639 -- 100.0
X Ray Diffraction 2.0163 2.3079 -- 135 2658 0.1446 0.1882 -- 99.0
X Ray Diffraction 2.3079 2.9068 -- 121 2654 0.1612 0.1793 -- 97.0
X Ray Diffraction 2.9068 23.2693 -- 127 2730 0.1709 0.2012 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.4049
Anisotropic B[1][1] -2.417
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.291
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.708
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.147
f_plane_restr 0.008
f_chiral_restr 0.106
f_angle_d 1.272
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 905
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 178

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: dev_723) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA data reduction
Mosflm data collection