X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 293.0
Details 17% PEG3350, 1.6 M LiCl, 0.1 M Tris, pH 9.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.56 α = 90
b = 132.61 β = 109.28
c = 122.81 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2011-07-14
Diffraction Radiation
Monochromator Protocol
Double crystal SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.98 CLSI 08ID-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
1.7 32.11 92.0 -- 0.059 -- 3.5 284036 284036 2.0 2.0 --
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)
1.7 1.79 80.3 0.201 0.201 3.7 3.2 36029

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
-- 1.7 32.107 -- 0.0 -- 283868 14327 91.73 -- 0.1362 0.1344 0.1704 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 1.7 1.744 -- 923 17148 0.165 0.22 -- 79.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.2787
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.5
Anisotropic B[2][2] -0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.84
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.024
r_dihedral_angle_2_deg 36.351
r_angle_refined_deg 2.322
r_dihedral_angle_3_deg 14.127
r_chiral_restr 0.199
r_dihedral_angle_1_deg 6.38
r_dihedral_angle_4_deg 13.761
r_gen_planes_refined 0.015
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.052
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22972
Nucleic Acid Atoms 0
Heterogen Atoms 176
Solvent Atoms 3053

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10