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 Experiment
ID # Data Collection Temperature
1 108
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4r mirrors 2000-06-07
CCD ADSC QUANTUM 1 mirrors 2000-08-21
Diffraction Radiation
Monochromator Protocol
parabolic collimating mirror SINGLE WAVELENGTH
parabolic collimating mirror MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER 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_bond_d 0.018
c_angle_deg 2.1
c_improper_angle_d 1.88
c_dihedral_angle_d 17.1
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

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