X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.81 α = 105.05
b = 63.31 β = 107.88
c = 65.66 γ = 113.03
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2014-04-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.979490 Diamond I04

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
2.33 52.5 97.0 0.041 -- -- 2.7 -- 33087 -- -- --
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)
2.33 2.39 96.4 0.588 -- -- 2.8 2428

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 2.33 50.0 -- -- -- 31606 1471 96.99 -- 0.19081 0.18802 0.2469 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 2.33 2.39 -- 104 2317 0.313 0.35 -- 96.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.06
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] -0.09
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] -0.04
Anisotropic B[3][3] 0.26
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_other 4.48
r_scbond_it 4.484
r_gen_planes_refined 0.008
r_bond_other_d 0.004
r_angle_other_deg 1.018
r_angle_refined_deg 1.566
r_long_range_B_other 7.629
r_mcbond_it 3.836
r_dihedral_angle_3_deg 15.941
r_mcangle_other 5.215
r_gen_planes_other 0.003
r_long_range_B_refined 7.63
r_mcbond_other 3.837
r_bond_refined_d 0.014
r_dihedral_angle_2_deg 38.395
r_chiral_restr 0.092
r_scangle_other 6.305
r_dihedral_angle_4_deg 21.04
r_dihedral_angle_1_deg 6.65
r_mcangle_it 5.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5083
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 18

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
xia2 data reduction
xia2 data scaling
PHASER phasing