X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % (w/v) PEG6K, protein dimer/DNA molar ratio 1:2, protein concentration 1.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.2 α = 90
b = 62.2 β = 90
c = 147.8 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-11-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.93930 ESRF ID14-4

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
2.3 50.61 99.9 0.111 -- -- 6.0 14413 14402 -- 2.0 29.7
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)
2.3 2.39 100.0 0.557 -- 3.2 6.1 1642

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 50.61 -- -- 13586 13576 773 99.9 -- 0.17309 0.17176 0.19647 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 2.3 2.36 1020 39 1020 0.264 0.299 -- 99.62
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 36.251
Anisotropic B[1][1] -0.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.47
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 4.59
r_bond_refined_d 0.006
r_chiral_restr 0.065
r_dihedral_angle_2_deg 37.746
r_dihedral_angle_4_deg 16.31
r_angle_refined_deg 1.036
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1541
Nucleic Acid Atoms 855
Heterogen Atoms 0
Solvent Atoms 57

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
REFMAC refinement version: 5.7.0029
MOSFLM data reduction
SCALA data scaling