X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 297.15
Details 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer System 3(Tris base; BICINE) 8.5, 50 % v/v Precipitant Mix 4(25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.54 α = 90
b = 44.64 β = 97.67
c = 42.24 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 RAYONIX MX-225 -- 2015-06-09
Diffraction Radiation
Monochromator Protocol
Si (111) and Si (220) Double crystal monochromato SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.978690 RRCAT INDUS-2 PX-BL21

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
2.2 33.82 98.7 0.091 -- -- 7.2 -- 9075 -- -- 29.45
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)
2.2 2.27 90.8 0.341 -- -- 5.1 --

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
SAD 2.2 15.28 -- 0.0 -- 9046 465 98.69 -- 0.1829 0.1807 0.2239 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 2.2 2.46 -- 126 2334 0.1852 0.2532 -- 95.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.43
Anisotropic B[1][1] 6.3899
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.5328
Anisotropic B[2][2] -1.7618
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6281
RMS Deviations
Key Refinement Restraint Deviation
t_omega_torsion 2.98
t_other_torsion 19.5
t_angle_deg 1.0
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.269
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1306
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 97

Software

Software
Software Name Purpose
BUSTER refinement version: 2.10.2
XDS data reduction
Aimless data scaling
XDS data scaling
PHENIX phasing