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 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.56 α = 90
b = 120.08 β = 111.68
c = 56.76 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 96
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-02-10
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C

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
2.07 50 81.5 -- -- -- -- 36750 36750 0.0 0.0 --
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)
2.07 2.12 71.5 -- -- -- -- --

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 39.503 -- 1.35 27711 27710 1409 85.21 -- 0.2079 0.2055 0.2521 --
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 2.3822 -- 58 1046 0.3515 0.448 -- 34.0
X Ray Diffraction 2.3822 2.4776 -- 98 1966 0.3078 0.3662 -- 64.0
X Ray Diffraction 2.4776 2.5903 -- 129 2449 0.3019 0.3179 -- 79.0
X Ray Diffraction 2.5903 2.7269 -- 140 2931 0.2931 0.3257 -- 95.0
X Ray Diffraction 2.7269 2.8977 -- 157 2973 0.27 0.3396 -- 97.0
X Ray Diffraction 2.8977 3.1213 -- 165 2986 0.2386 0.3086 -- 97.0
X Ray Diffraction 3.1213 3.4353 -- 151 2968 0.2 0.2434 -- 96.0
X Ray Diffraction 3.4353 3.932 -- 155 3001 0.169 0.2183 -- 97.0
X Ray Diffraction 3.932 4.9523 -- 159 3013 0.1408 0.1941 -- 97.0
X Ray Diffraction 4.9523 39.509 -- 197 2968 0.1715 0.2018 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.0212
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.1008
Anisotropic B[2][2] -6.2184
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.3667
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.048
f_dihedral_angle_d 20.272
f_angle_d 0.77
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2527
Nucleic Acid Atoms 650
Heterogen Atoms 2
Solvent Atoms 363

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1005) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
ADSC version: Quantum data collection