X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 290.0
Details 11% PEG 8000, 10 mM magnesium sulfate, 100 mM bis-tris-propane, pH 7, VAPOR DIFFUSION, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 257.51 α = 90
b = 257.51 β = 90
c = 257.51 γ = 90
Symmetry
Space Group P 43 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors --
Diffraction Radiation
Monochromator Protocol
Si 220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.005 APS 22-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
3.3 91.04 98.9 0.096 0.096 -- 9.1 43653 43653 -- -3.0 --
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)
3.3 3.39 99.7 0.461 0.461 1.6 7.7 3211

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
FOURIER SYNTHESIS 3.3 20.0 -- 0.0 -- 43392 2219 98.47 -- 0.255 0.253 0.291 --
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 3.3 3.383 3107 168 2939 0.285 0.324 -- 99.58
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS refinement by domains
Mean Isotropic B 103.516
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.315
r_dihedral_angle_1_deg 2.375
r_dihedral_angle_4_deg 12.695
r_symmetry_hbond_refined 0.25
r_scangle_it 1.079
r_gen_planes_refined 0.004
r_chiral_restr 0.096
r_symmetry_vdw_refined 0.155
r_dihedral_angle_3_deg 10.969
r_dihedral_angle_2_deg 23.021
r_angle_refined_deg 1.367
r_nbd_refined 0.184
r_mcangle_it 0.527
r_mcbond_it 0.297
r_scbond_it 0.614
r_xyhbond_nbd_refined 0.182
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13939
Nucleic Acid Atoms 610
Heterogen Atoms 28
Solvent Atoms 10

Software

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345dtb data collection
XDS data reduction
REFMAC phasing version: 5.2.005