X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 0.1 M Tris, 50-125 mM sodium acetate and 20-24% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 172.5 α = 90
b = 172.5 β = 90
c = 34.09 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Rh coated flat mirror 2012-05-08
Diffraction Radiation
Monochromator Protocol
Side scattering I-beam bent single crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.23 SSRL BL7-1

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
3.7 100 96.7 -- 0.105 -- 1.9 12778 6475 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)
3.7 3.8 95.6 -- 0.39 1.92 1.8 598

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 3.7 100.0 -- 2.0 6475 6169 306 98.51 -- 0.30252 0.3019 0.31564 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 3.7 3.796 422 18 404 0.344 0.404 -- 94.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.623
Anisotropic B[1][1] 1.39
Anisotropic B[1][2] 0.69
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.08
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 40.246
r_angle_refined_deg 2.07
r_dihedral_angle_4_deg 25.009
r_gen_planes_refined 0.014
r_bond_refined_d 0.019
r_chiral_restr 0.111
r_dihedral_angle_1_deg 6.072
r_dihedral_angle_3_deg 26.93
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3121
Nucleic Acid Atoms 410
Heterogen Atoms 2
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
REFMAC refinement version: 5.6.0117
HKL-2000 data reduction
SCALEPACK data scaling