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 = 156.55 α = 90
b = 220.33 β = 97
c = 191.56 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
3.95 50 98.4 0.255 -- 5.774 5.1 -- 54937 -- -- --
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)
3.95 4.02 97.7 0.937 -- -- 4.7 2692

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 3.96 50.0 -- 0.0 -- 47410 2560 88.95 -- 0.2513 0.2489 0.2964 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 3.958 4.06 -- 135 2689 0.338 0.391 -- 68.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 147.355
Anisotropic B[1][1] 25.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -13.07
Anisotropic B[2][2] -6.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.49
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_dihedral_angle_2_deg 39.9
r_dihedral_angle_4_deg 19.886
r_angle_other_deg 3.67
r_mcangle_it 10.227
r_dihedral_angle_1_deg 9.224
r_chiral_restr 0.084
r_gen_planes_refined 0.006
r_angle_refined_deg 1.484
r_dihedral_angle_3_deg 24.242
r_mcbond_other 6.023
r_bond_other_d 0.0
r_bond_refined_d 0.008
r_mcbond_it 6.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28121
Nucleic Acid Atoms 419
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
PHENIX refinement
Coot model building