X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 288.2
Details PEG 4000, Magnesium Choloride, Sodium Chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.2K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.86 α = 90
b = 63.86 β = 90
c = 92.07 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 MIRROR 1999-07-23
Diffraction Radiation
Monochromator Protocol
Silicon (111) Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.92000 NSLS X9B

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 27.65 99.4 0.039 0.056 -- 5.88 15110 14820 0.0 -3.0 26.9
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)
2.0 2.07 99.9 0.389 0.41 4.64 5.8 1461

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 2.0 30.0 -- 0.0 14820 14820 739 97.8 -- -- 0.217 0.252 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 2.0 2.13 1592 121 2242 0.274 0.298 0.027 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.1
Anisotropic B[1][1] 3.76
Anisotropic B[1][2] -0.78
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.52
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 20.2
c_scangle_it 4.31
c_bond_d 0.006
c_mcangle_it 2.87
c_angle_deg 1.2
c_scbond_it 3.01
c_improper_angle_d 0.81
c_mcbond_it 1.99
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1226
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 173

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing