X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 25% (w/v) PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-TRIS propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.43 α = 90
b = 27.64 β = 114.14
c = 67.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2012-01-09
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
1.46 33.7 98.9 3.8 -- -- -- 34254 34254 2.8 2.8 --
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)
1.456 1.493 98.9 0.038 0.038 2.8 2.0 34254

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 1.46 33.7 2.8 2.8 32519 32519 1728 98.85 -- 0.16525 0.16239 0.21813 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 1.456 1.493 32519 1728 2000 0.1653 0.218 -- 98.9
X Ray Diffraction 1.493 1.53 4636 117 -- 0.273 0.319 -- 94.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.55
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.22
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.47
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.082
r_sphericity_free 31.242
r_rigid_bond_restr 3.062
r_dihedral_angle_4_deg 16.443
r_sphericity_bonded 10.183
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 11.252
r_bond_other_d 0.001
r_angle_refined_deg 1.44
r_angle_other_deg 0.928
r_gen_planes_refined 0.006
r_bond_refined_d 0.009
r_dihedral_angle_1_deg 5.659
r_dihedral_angle_2_deg 34.598
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.081
Luzzati ESD (R-Free Set) 0.077
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1455
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 309

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
REFMAC refinement version: 5.6.0117
XDS data reduction
SCALA data scaling