X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 288.0
Details PEG 4000, magnesium choloride, sodium chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, NAHEPES, PLATINUM POTASSIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.83 α = 90
b = 63.83 β = 90
c = 91.92 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 1999-08-03
Diffraction Radiation
Monochromator Protocol
Silicon (111) Channel MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 1.07223,1.07186,1.06268,1.08121 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
1.8 19.02 99.7 0.104 0.08 -- 6.64 20677 20594 0.0 -3.0 23.2
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)
1.8 1.86 99.8 0.176 0.165 4.34 5.86 2035

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
MAD 1.8 20.0 0.0 0.0 20594 20594 999 99.7 -- -- 0.221 0.249 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 1.83 2035 49 1029 0.275 0.3026 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.9
Anisotropic B[1][1] 2.67
Anisotropic B[1][2] -0.32
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.34
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.97
c_improper_angle_d 0.75
c_mcangle_it 1.99
c_scbond_it 2.01
c_bond_d 0.005
c_angle_deg 1.1
c_dihedral_angle_d 20.1
c_mcbond_it 1.27
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1226
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 194

Software

Software
Software Name Purpose
PHASES phasing
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling