X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details 50 mM NaI, 27% (w/v) PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.86 α = 90
b = 98.81 β = 90
c = 100.75 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 ADSC QUANTUM 315r Asymmetric cut single crystal Si (220) 2009-06-24
Diffraction Radiation
Monochromator Protocol
Asymmetric cut single crystal Si (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1

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
2.3 50 99.9 0.087 -- -- 6.4 35447 35447 -- -- --
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)
2.3 2.34 99.3 0.545 -- -- 6.2 --

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 2.3 49.407 -- 0.0 35447 32385 1629 93.14 -- 0.1844 0.1806 0.2532 --
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 2.3 2.3677 -- 113 2331 0.194 0.2569 -- 86.0
X Ray Diffraction 2.3677 2.4442 -- 137 2379 0.1837 0.2963 -- 88.0
X Ray Diffraction 2.4442 2.5315 -- 105 2452 0.1847 0.2635 -- 90.0
X Ray Diffraction 2.5315 2.6329 -- 113 2413 0.171 0.2627 -- 88.0
X Ray Diffraction 2.6329 2.7527 -- 134 2425 0.1912 0.2655 -- 89.0
X Ray Diffraction 2.7527 2.8978 -- 138 2422 0.2009 0.3133 -- 89.0
X Ray Diffraction 2.8978 3.0793 -- 130 2541 0.208 0.2972 -- 92.0
X Ray Diffraction 3.0793 3.317 -- 145 2699 0.2021 0.2877 -- 99.0
X Ray Diffraction 3.317 3.6507 -- 157 2736 0.1882 0.3018 -- 99.0
X Ray Diffraction 3.6507 4.1788 -- 129 2693 0.1589 0.2619 -- 97.0
X Ray Diffraction 4.1788 5.2639 -- 162 2755 0.1398 0.1753 -- 99.0
X Ray Diffraction 5.2639 49.4184 -- 166 2910 0.1941 0.2133 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.2925
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.3837
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.0913
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_bond_d 0.007
f_dihedral_angle_d 12.568
f_chiral_restr 0.067
f_angle_d 1.047
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5423
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 400

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum
HKL-2000 data reduction
MOLREP phasing