X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details VAPOR DIFFUSION, HANGING DROP AT 277 K. MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.50. 80 uM Pactamycin soaked into preformed crystals.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 401.72 α = 90
b = 401.72 β = 90
c = 177 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-07-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.93950 ESRF ID14-4

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
3.4 99 94.4 -- 0.125 -- 3.75 184902 184902 0.0 0.0 85.45
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)
3.4 3.52 90.7 -- 0.424 2.34 2.4 17552

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
FOURIER SYNTHESIS 3.4 95.34 0.0 0.0 175113 175113 8776 88.9 -- 0.232 0.232 0.28 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 3.4 3.52 -- 779 15082 0.3046 0.3406 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 75.36
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.56
c_bond_d 0.007
c_angle_deg 1.25
c_dihedral_angle_d 28.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.51
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19264
Nucleic Acid Atoms 32508
Heterogen Atoms 138
Solvent Atoms 0

Software

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