X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 298.0
Details Tris, ATP, MgCl2, DTT, Hexanediol, PEG4000, LiSO4, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.83 α = 90
b = 78.11 β = 90
c = 90.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2000-06-10
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID

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
2.3 20 99.7 0.09 -- -- 6.0 13208 13178 1.0 1.0 17.3
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)
2.3 2.44 74.7 0.185 -- 5.0 4.0 1607

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 2.3 20.0 -- 1.0 13208 13178 669 -- 0.26 0.258 0.258 0.292 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 2.3 2.44 1607 79 -- 0.267 0.31 0.041 74.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.4
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.31
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.5
c_mcbond_it 1.51
c_improper_angle_d 0.85
c_dihedral_angle_d 22.6
c_angle_deg 1.5
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.034
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.039
Luzzati Sigma A (R-Free Set) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2418
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 146

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
AMoRE model building
SCALEPACK data reduction
HKL-2000 data collection