X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 5 mg/ml HexB [final], 50% saturated ammonium sulfate, 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.41 α = 90
b = 112.41 β = 90
c = 397.23 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 bent conical Si-mirror (Rh coating) 2001-12-06
Diffraction Radiation
Monochromator Protocol
bent cylindrical Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C

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
2.5 37 -- -- -- -- -- -- 52315 -- -3.0 --

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 2.5 36.76 -- 0.0 -- 49713 2597 100.0 -- 0.19964 0.1982 0.22671 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 2.5 2.565 -- 206 3503 0.223 0.279 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.379
Anisotropic B[1][1] 2.47
Anisotropic B[1][2] 1.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.492
r_chiral_restr 0.092
r_mcangle_it 0.921
r_scangle_it 2.368
r_angle_other_deg 1.175
r_mcbond_it 0.475
r_nbd_other 0.142
r_xyhbond_nbd_refined 0.152
r_symmetry_hbond_refined 0.147
r_symmetry_vdw_refined 0.124
r_dihedral_angle_1_deg 4.297
r_symmetry_vdw_other 0.147
r_bond_other_d 0.003
r_angle_refined_deg 1.557
r_symmetry_hbond_other 0.073
r_bond_refined_d 0.011
r_nbd_refined 0.181
r_gen_planes_refined 0.005
r_nbtor_other 0.48
r_dihedral_angle_3_deg 18.192
r_gen_planes_other 0.003
r_xyhbond_nbd_other 0.066
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7756
Nucleic Acid Atoms 0
Heterogen Atoms 107
Solvent Atoms 244

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement