X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details MPD, magnesium acetate, sodium cacodylate, spermine tetrahydrochloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.64 α = 90
b = 39.64 β = 90
c = 98.59 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 1 mirrors 2000-08-21
CCD ADSC QUANTUM 4r mirrors 2000-06-07
Diffraction Radiation
Monochromator Protocol
parabolic collimating mirror MAD
parabolic collimating mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE CCD Quantum1 1.5418 -- --
SYNCHROTRON NSLS BEAMLINE X8C 1.0722 NSLS X8C

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
2.1 13 94.6 0.064 -- -- 9.9 5576 54956 4.0 -- 34.6
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)
2.1 2.14 99.6 0.234 -- -- 8.3 269

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 2.1 13.0 -- 4.0 -- 5310 518 94.6 -- 0.237 0.237 0.266 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 2.1 2.23 -- 84 717 0.318 0.362 0.04 88.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.6
Anisotropic B[1][1] -2.59
Anisotropic B[1][2] -13.62
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.18
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.88
c_dihedral_angle_d 17.1
c_angle_deg 2.1
c_bond_d 0.018
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 486
Heterogen Atoms 0
Solvent Atoms 100

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
MLPHARE model building
SCALEPACK data reduction
DENZO data collection