X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microseeding
pH 7.5
Temperature 294.0
Details PEG 4000, ammonium acetate, glycerol, DTT, Hepes, Microseeding, pH 7.5 at 294 K, microseeding

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.43 α = 90
b = 172.51 β = 117.36
c = 79.99 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
2 123
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirror 2000-07-02
CCD ADSC QUANTUM 4 -- 2000-05-04
Diffraction Radiation
Monochromator Protocol
horizontally bent Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.942 CHESS F1
SYNCHROTRON ALS BEAMLINE 5.0.1 1.1 ALS 5.0.1

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
2.1 100 97.6 0.072 -- -- 5.0 101858 101858 -- -3.0 27.1
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)
2.1 2.14 87.6 0.473 -- 1.3 2.0 4532

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
difference fourier 2.1 43.29 -3.0 -- 101733 101733 2006 97.6 -- -- 0.219 0.239 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 2.1 2.23 -- 329 15422 0.329 0.314 0.017 91.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 55.4
Anisotropic B[1][1] 1.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 13.25
Anisotropic B[2][2] -4.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.75
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.65
c_scbond_it 1.07
c_mcangle_it 1.21
c_mcbond_it 0.7
c_improper_angle_d 1.35
c_dihedral_angle_d 23.1
c_angle_deg 1.7
c_bond_d 0.087
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11764
Nucleic Acid Atoms 0
Heterogen Atoms 213
Solvent Atoms 182

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building