X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details PEG 4000, Sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.32 α = 90
b = 129.32 β = 90
c = 33.12 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 170
2 170
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 -- 2001-03-01
CCD BRANDEIS - B4 -- 2001-04-13
Diffraction Radiation
Monochromator Protocol
Si (111) MAD
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.94207, 0.97941, 0.97927 APS 19-ID
SYNCHROTRON NSLS BEAMLINE X25 0.9188 NSLS X25

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
1.8 50 95.5 0.036 -- -- -- -- 19192 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)
1.8 50.0 74.6 0.33 -- 3.2 -- --

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 1.8 40.0 0.0 0.0 19192 18277 1257 88.8 0.231 0.231 0.229 0.244 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 1.8 1.86 1352 107 -- 0.3613 0.3761 0.77 70.27
X Ray Diffraction 1.86 1.94 1573 121 -- 0.3177 0.3787 0.79 81.17
X Ray Diffraction 1.94 2.03 1737 105 -- 0.2909 0.2911 0.85 91.66
X Ray Diffraction 2.03 2.13 1746 131 -- 0.2708 0.2655 0.89 91.7
X Ray Diffraction 2.13 2.27 1807 128 -- 0.2599 0.2981 0.86 93.24
X Ray Diffraction 2.27 2.44 1773 130 -- 0.2436 0.293 0.88 93.02
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.6956
c_dihedral_angle_d 18.5541
c_mcbond_it 1.407
c_bond_d 0.00766
c_angle_deg 1.01337
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1355
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 163

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CNS refinement
HKL-2000 data reduction
CNS phasing