X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Temperature 298.0
Details 0.1M TRIS, 20% PEG3350 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.47 α = 90
b = 175.47 β = 90
c = 34.32 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 MIRROR 2011-11-11
Diffraction Radiation
Monochromator Protocol
DOUBLE-CRYSTAL, SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 -- ALS 5.0.2

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
3.1 50 99.7 0.078 -- -- 8.9 -- 11516 -- 2.0 --

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 3.1 43.87 -- 0.0 11516 11319 248 99.3 -- 0.24 0.238 0.268 --
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 3.1028 3.415 -- 137 2596 0.2935 0.3513 -- 98.0
X Ray Diffraction 3.415 3.9089 -- 133 2664 0.2727 0.3122 -- 100.0
X Ray Diffraction 3.9089 4.9237 -- 141 2698 0.2263 0.268 -- 100.0
X Ray Diffraction 4.9237 43.8724 -- 132 2818 0.2122 0.2209 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 76.2
Anisotropic B[1][1] 9.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.49
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.013
f_chiral_restr 0.089
f_dihedral_angle_d 21.751
f_angle_d 2.157
f_bond_d 0.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.55
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3148
Nucleic Acid Atoms 410
Heterogen Atoms 2
Solvent Atoms 16

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
CNS version: 1.3 refinement