X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 20% PEG3350, 0.2 M diammonium citrate, cryoprotectant: Paratone N, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.42 α = 90
b = 123.87 β = 90.97
c = 125.6 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 315 -- 2011-02
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-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
2.15 125.58 99.9 -- 0.061 -- 6.5 60928 60928 -- -- --
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)
2.15 2.27 100.0 0.301 0.301 2.4 6.6 8872

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
SAD 2.15 28.377 -- 0.0 -- 59609 3025 97.75 -- 0.1927 0.1903 0.2361 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 2.15 2.206 -- 232 4012 0.233 0.314 -- 94.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.4834
Anisotropic B[1][1] -1.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.59
Anisotropic B[2][2] 0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.56
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.611
r_scbond_it 3.142
r_mcangle_it 2.022
r_mcbond_other 0.271
r_bond_refined_d 0.022
r_bond_other_d 0.001
r_angle_refined_deg 1.717
r_angle_other_deg 1.013
r_dihedral_angle_1_deg 6.75
r_dihedral_angle_2_deg 37.931
r_dihedral_angle_3_deg 16.374
r_dihedral_angle_4_deg 14.421
r_chiral_restr 0.111
r_gen_planes_refined 0.009
r_gen_planes_other 0.001
r_mcbond_it 1.118
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7401
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 485

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0102 refinement
SCALA version: 3.3.15 data reduction