X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 277.0
Details 0.06% n-decylpentaoxyethylene (c10e5), 12% (w/v) PEG 3000, 0.1 M lithium sulfate, 0.1 M N-(2-acetamido)iminodiacetic acid (ADA), 2% (v/v) isopropanol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.37 α = 90
b = 97.37 β = 90
c = 171.94 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 TOROIDAL MIRROR 2002-05-04
Diffraction Radiation
Monochromator Protocol
DIAMOND (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1

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
2.55 40 98.6 0.07 0.07 -- 12.1 10503 10350 -3.7 -3.7 69.8
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)
2.55 2.64 99.7 0.375 0.375 5.2 8.7 1029

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 2.55 30.15 0.0 0.0 10340 10340 501 100.0 -- 0.22664 0.22514 0.25791 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 2.55 2.616 -- 39 694 0.236 0.452 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 39.103
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] -0.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.59
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.351
r_chiral_restr 0.099
r_gen_planes_refined 0.005
r_bond_refined_d 0.016
r_scbond_it 2.018
r_symmetry_hbond_refined 0.094
r_nbd_other 0.244
r_angle_other_deg 0.796
r_symmetry_vdw_other 0.184
r_gen_planes_other 0.003
r_mcbond_it 0.684
r_dihedral_angle_1_deg 8.318
r_angle_refined_deg 1.739
r_scangle_it 3.33
r_symmetry_vdw_refined 0.123
r_bond_other_d 0.002
r_nbd_refined 0.2
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1161
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 9

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing