X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 293.0
Details 0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% PEG 8000, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.48 α = 90
b = 38.74 β = 101.13
c = 73.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U

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
1.78 72.07 97.4 -- 0.064 -- 5.2 27836 27836 -- -- --
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)
1.78 1.88 96.4 0.129 0.129 5.2 5.3 3973

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
MOLECULAR REPLACEMENT 1.78 34.12 -- 0.0 -- 27834 1407 97.04 -- 0.1713 0.1687 0.2213 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 1.78 1.826 -- 92 1823 0.185 0.239 -- 95.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.4674
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.27
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.16
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.13
r_dihedral_angle_4_deg 15.518
r_dihedral_angle_3_deg 13.332
r_dihedral_angle_2_deg 34.794
r_dihedral_angle_1_deg 6.096
r_angle_other_deg 0.942
r_angle_refined_deg 1.732
r_bond_other_d 0.007
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2111
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 247

Software

Computing
Computing Package Purpose
SCALA Data Reduction (data scaling)
Balbes Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALA version: 3.3.20 data reduction