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

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_mcbond_it 1.407
c_improper_angle_d 0.6956
c_dihedral_angle_d 18.5541
c_angle_deg 1.01337
c_bond_d 0.00766
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

Computing
Computing Package Purpose
HKL-2000 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
HKL-2000 data collection