X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 291.0
Details PEG 4000, potassium phosphate, thiamin diphosphate, FAD, magnesium chloride, DTT, ammonium acetate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.55 α = 90
b = 109.4 β = 90
c = 178.86 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2000-12-17
Diffraction Radiation
Monochromator Protocol
Ge(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.00 APS 14-BM-C

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
2.6 50 97.8 0.058 -- -- 3.7 214515 214515 0.0 0.0 --
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)
2.6 2.69 99.2 0.301 -- 3.9 3.6 5733

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 2.6 100.0 0.0 0.0 54927 54927 5574 94.1 0.191 0.191 0.188 0.219 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 2.6 2.7 4664 496 4664 0.247 0.267 0.0 90.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Anisotropic B[1][1] 1.245
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.228
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.983
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.794
c_dihedral_angle_d 22.45
c_bond_d 0.006
c_angle_deg 1.274
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8126
Nucleic Acid Atoms 0
Heterogen Atoms 177
Solvent Atoms 325

Software

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