X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 292.0
Details 0.1M Sodium Citrate, 5% PEG 6000, pH 4, vapor diffusion, sitting drop, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.88 α = 90
b = 81.76 β = 90
c = 115.13 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 315 -- 2009-02-01
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02

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
2.6 41 98.6 0.073 0.085 -- 3.5 13996 13088 0.0 3.0 58.0
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)
2.6 2.74 99.4 0.307 0.362 3.6 3.6 1899

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 2.6 41.0 -- 1.09 24606 23671 1167 96.2 -- 0.1954 0.1914 0.2687 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 2.6 2.7183 -- 114 2902 0.2537 0.3582 -- 98.0
X Ray Diffraction 2.7183 2.8616 -- 155 2814 0.2405 0.3302 -- 97.0
X Ray Diffraction 2.8616 3.0408 -- 143 2815 0.2217 0.325 -- 97.0
X Ray Diffraction 3.0408 3.2755 -- 174 2822 0.2074 0.3052 -- 97.0
X Ray Diffraction 3.2755 3.605 -- 158 2827 0.1742 0.2954 -- 97.0
X Ray Diffraction 3.605 4.1262 -- 115 2833 0.1625 0.2315 -- 96.0
X Ray Diffraction 4.1262 5.197 -- 138 2797 0.129 0.2017 -- 96.0
X Ray Diffraction 5.197 41.0 -- 170 2694 0.1764 0.2171 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 49.8
Anisotropic B[1][1] -4.1859
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.7462
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.5603
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.081
f_chiral_restr 0.078
f_plane_restr 0.004
f_bond_d 0.008
f_dihedral_angle_d 18.869
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3290
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 36

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.4_129)
MOSFLM data reduction
SCALA data scaling