X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 291.0
Details 25% PEG3350, 0.2 M amonium sulfate, 0.1 M bis-tris, pH 6.5, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.73 α = 90
b = 39.75 β = 103.56
c = 56.24 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 2014-01-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
1.8 34.73 97.1 0.112 -- -- 3.6 -- 14029 -- -- --
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)
1.8 1.84 90.7 0.587 -- 2.3 3.3 773

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 1.8 30.0 -- 0.0 -- 14013 700 97.17 -- 0.2064 0.2034 0.2636 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 1.8 1.847 -- 48 932 0.266 0.291 -- 94.41
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.3503
Anisotropic B[1][1] -1.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.74
Anisotropic B[2][2] -1.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.28
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_mcbond_it 1.826
r_dihedral_angle_3_deg 11.705
r_chiral_restr 0.077
r_dihedral_angle_1_deg 6.206
r_mcbond_other 1.825
r_angle_refined_deg 1.371
r_dihedral_angle_4_deg 15.135
r_mcangle_it 2.749
r_dihedral_angle_2_deg 31.952
r_angle_other_deg 0.792
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1275
Nucleic Acid Atoms 106
Heterogen Atoms 7
Solvent Atoms 89

Software

Software
Software Name Purpose
Aimless data scaling version: 0.2.17
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.14
XDS data reduction