X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.6M ammonium sulfate, 2% polyethyleneglycol 400, 0.1M Tris-HCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.75 α = 90
b = 86.75 β = 90
c = 146.52 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2009-03-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 6C1 0.979 PAL/PLS 6C1

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
2.6 20 100.0 0.122 -- -- 13.8 -- 17839 -- -- --
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)
2.6 2.64 100.0 0.76 -- -- 13.9 880

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 2.6 19.82 -- 0.0 -- 17777 910 99.71 -- 0.246 0.244 0.292 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 2.601 2.667 -- 66 1189 0.312 0.413 -- 97.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.479
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 38.715
r_angle_refined_deg 1.485
r_scangle_it 2.867
r_mcbond_it 0.808
r_nbtor_refined 0.317
r_dihedral_angle_4_deg 20.753
r_symmetry_vdw_refined 0.306
r_symmetry_hbond_refined 0.296
r_scbond_it 1.789
r_chiral_restr 0.102
r_gen_planes_refined 0.005
r_mcangle_it 1.434
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 18.847
r_nbd_refined 0.25
r_xyhbond_nbd_refined 0.171
r_dihedral_angle_1_deg 6.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2696
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 68

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005