X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details Hampton research SaltRX condition #96: 0.1M Bis-Tris Propane buffer, 60% Tascimate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.99 α = 90
b = 119.99 β = 90
c = 249.75 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY 2006-04-01
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D -- APS 23-ID-D

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 50 98.7 0.047 -- -- 5.6 -- 42052 -- 0.0 --
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)
3.0 3.11 98.3 0.36 -- 2.1 5.6 --

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 3.0 20.0 -- 0.0 41581 39493 2088 98.2 -- 0.186 0.185 0.211 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 3.0 3.08 -- 147 2775 0.293 0.335 -- 95.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.66
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.34
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.374
r_scbond_it 1.238
r_symmetry_vdw_refined 0.192
r_bond_refined_d 0.01
r_scangle_it 1.857
r_angle_refined_deg 1.047
r_xyhbond_nbd_refined 0.123
r_nbd_refined 0.225
r_symmetry_hbond_refined 0.185
r_dihedral_angle_1_deg 4.871
r_chiral_restr 0.075
r_mcbond_it 0.537
r_dihedral_angle_2_deg 35.909
r_gen_planes_refined 0.003
r_nbtor_refined 0.322
r_mcangle_it 0.733
r_dihedral_angle_3_deg 19.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9358
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 6

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing