X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 25% saturated ammonium sulfate, 0.1 M Tris-chloride, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.81 α = 90
b = 94.03 β = 90
c = 104.28 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE -- -- 1999-06-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.78 SSRL BL9-1

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
0.97 14.46 99.8 0.076 -- -- -- 135318 135318 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)
0.97 0.99 99.6 0.997 -- -- -- 6691

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 1.0 14.45 -- 0.0 117375 117375 6225 99.74 -- 0.1195 0.1182 0.1432 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 1.0 1.026 -- 411 8257 0.215 0.221 -- 99.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.9907
Anisotropic B[1][1] -0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 9.412
r_dihedral_angle_1_deg 7.197
r_sphericity_free 15.885
r_angle_other_deg 0.91
r_dihedral_angle_3_deg 12.0
r_gen_planes_other 0.002
r_gen_planes_refined 0.007
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_rigid_bond_restr 2.185
r_dihedral_angle_2_deg 28.175
r_angle_refined_deg 1.574
r_chiral_restr 0.092
r_sphericity_bonded 7.359
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1842
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 331

Software

Software
Software Name Purpose
SCALEPACK data scaling
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
DENZO data reduction