X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 318.15
Details 3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 290.26 α = 90
b = 332.11 β = 94.08
c = 337.7 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-09-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 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
3.5 100 75.3 0.08 -- -- 4.0 -- 597062 4.0 2.0 12.7
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)
3.5 3.63 54.6 0.115 -- 18.0 2.6 43298

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 3.5 82.45 -- 0.0 597050 597050 59662 74.6 -- -- 0.232 0.234 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 3.5 3.66 -- 5469 49477 0.275 0.281 0.004 55.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Anisotropic B[1][1] 0.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 26.04
Anisotropic B[2][2] -5.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.36
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.25
c_bond_d 0.017
c_angle_deg 1.6
c_dihedral_angle_d 24.9
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4983
Nucleic Acid Atoms 110
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
EPICS Data Reduction (intensity integration)
SNP Data Reduction (data scaling)
ENVELOPE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
ENVELOPE model building
SNP data reduction
EPICS data collection