X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 0.2M LiSO4, 25% PEG 3350, Hepes pH7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 158.75 α = 90
b = 158.75 β = 90
c = 158.75 γ = 90
Symmetry
Space Group F 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID

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
3.2 50 100.0 0.078 -- -- 11.2 -- 5601 -- -- --
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)
3.2 3.31 100.0 0.401 -- -- 11.4 551

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 3.2 47.89 -- 0.0 -- 5597 350 100.0 -- 0.242 0.238 0.297 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 3.201 3.284 -- 29 391 0.248 0.338 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.062
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.527
r_scbond_it 0.54
r_symmetry_vdw_refined 0.14
r_symmetry_vdw_other 0.192
r_xyhbond_nbd_refined 0.134
r_dihedral_angle_1_deg 4.498
r_bond_refined_d 0.007
r_angle_refined_deg 1.023
r_dihedral_angle_3_deg 16.659
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 15.222
r_chiral_restr 0.05
r_nbd_refined 0.214
r_gen_planes_refined 0.003
r_mcbond_other 0.039
r_nbtor_other 0.085
r_scangle_it 0.834
r_bond_other_d 0.001
r_angle_other_deg 0.713
r_nbtor_refined 0.18
r_nbd_other 0.16
r_mcangle_it 0.564
r_dihedral_angle_2_deg 35.357
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1840
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 25

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data collection
HKL-2000 data reduction