X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details PEG 6000, LiCl, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.55 α = 90
b = 47.65 β = 90
c = 129.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-02-06
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.931 ESRF ID14-4

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
1.2 64.6 99.7 -- 0.063 -- 4.1 89183 88916 0.0 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)
1.2 1.21 94.1 -- 0.272 3.5 2.3 --

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 1.2 50.0 -- 0.0 84491 84491 4306 100.0 0.14822 0.14822 0.14686 0.17451 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 1.2 1.231 -- 291 5899 0.162 0.178 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.873
Anisotropic B[1][1] 0.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.31
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.679
r_sphericity_free 15.439
r_rigid_bond_restr 1.825
r_scangle_it 5.31
r_scbond_it 3.739
r_mcangle_it 2.778
r_mcbond_it 1.899
r_symmetry_hbond_refined 0.224
r_symmetry_vdw_other 0.272
r_symmetry_vdw_refined 0.569
r_xyhbond_nbd_other 0.064
r_xyhbond_nbd_refined 0.14
r_bond_refined_d 0.023
r_bond_other_d 0.002
r_angle_refined_deg 2.384
r_angle_other_deg 3.181
r_dihedral_angle_1_deg 6.02
r_dihedral_angle_3_deg 15.784
r_chiral_restr 0.127
r_gen_planes_refined 0.009
r_gen_planes_other 0.004
r_nbd_refined 0.217
r_nbd_other 0.199
r_nbtor_other 0.274
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2275
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 378

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE V. 2.1, MLPHARE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement