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 = 116.98 α = 90
b = 119.44 β = 112.42
c = 56.92 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
2.4 50 77.7 -- -- -- -- 21996 21996 0.0 0.0 --

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 40.082 -- 0.0 21975 21975 1120 77.69 -- 0.2187 0.2159 0.2698 --
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 2.5092 -- 73 1301 0.2742 0.3671 -- 39.0
X Ray Diffraction 2.5092 2.6415 -- 76 1730 0.2726 0.3303 -- 51.0
X Ray Diffraction 2.6415 2.807 -- 103 2160 0.2939 0.3455 -- 64.0
X Ray Diffraction 2.807 3.0236 -- 162 2627 0.3018 0.3225 -- 79.0
X Ray Diffraction 3.0236 3.3278 -- 174 3123 0.2568 0.3212 -- 94.0
X Ray Diffraction 3.3278 3.809 -- 195 3308 0.2085 0.2964 -- 98.0
X Ray Diffraction 3.809 4.7977 -- 169 3278 0.1677 0.2165 -- 98.0
X Ray Diffraction 4.7977 40.088 -- 168 3328 0.1918 0.219 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.3904
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.9442
Anisotropic B[2][2] 3.9598
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.3502
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.05
f_dihedral_angle_d 19.632
f_angle_d 0.857
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2528
Nucleic Acid Atoms 593
Heterogen Atoms 23
Solvent Atoms 136

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