X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.15
Details 390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 167.15 α = 90
b = 220.8 β = 100.25
c = 193.92 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 315r -- 2013-10-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3

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
4.1 50 86.0 0.222 -- 4.375 2.7 -- 46515 -- -- --
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)
4.1 4.17 72.9 0.737 -- -- 2.2 1960

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 4.1 50.0 -- 0.0 -- 39147 2105 75.91 -- 0.2447 0.2423 0.2892 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 4.098 4.204 -- 88 1633 0.3 0.328 -- 42.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 86.315
Anisotropic B[1][1] 6.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -6.32
Anisotropic B[2][2] -2.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.25
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 20.3
r_gen_planes_refined 0.005
r_mcangle_it 6.528
r_angle_other_deg 3.673
r_chiral_restr 0.08
r_dihedral_angle_3_deg 23.993
r_bond_other_d 0.0
r_angle_refined_deg 1.443
r_gen_planes_other 0.003
r_bond_refined_d 0.008
r_dihedral_angle_2_deg 40.881
r_dihedral_angle_1_deg 8.813
r_mcbond_it 3.973
r_mcbond_other 3.973
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28132
Nucleic Acid Atoms 381
Heterogen Atoms 8
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.5.2
REFMAC refinement
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data scaling