X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.36 α = 90
b = 49.39 β = 103.87
c = 54.82 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 CLSI BEAMLINE 08ID-1 1.25 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
1.65 50 95.0 -- -- -- -- 164578 17542 2.0 2.0 28.8

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 1.8 20.58 -- 0.0 -- 17542 1533 94.2 -- -- 0.211 0.275 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 1.8 1.91 -- 87 2819 0.259 0.332 0.039 94.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.4906
Anisotropic B[1][1] 9.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.93
Anisotropic B[2][2] -10.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.7
c_dihedral_angle_d 15.6
c_angle_deg 0.9
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1810
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 352

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
CNS 1.3 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
CNS version: 1.3 refinement