X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details Mg acetate; MPD; Glycine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.5 α = 90
b = 88.5 β = 90
c = 105.08 γ = 120
Symmetry
Space Group P 62

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 -- 2001-01-28
CCD SBC-2 -- 2001-08-18
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97936,0.97950,1.008 APS 19-ID
SYNCHROTRON APS BEAMLINE 19-ID 0.97934 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
1.9 50 100.0 0.078 -- -- 6.0 36818 36818 0.0 -3.0 16.6
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)
1.9 1.97 100.0 0.677 -- 3.0 5.0 3693

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 1.9 36.0 -- 0.0 36818 36763 1823 99.8 -- 0.201 0.201 0.235 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 1.9 2.02 -- 298 5832 0.254 0.297 0.017 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.8
Anisotropic B[1][1] -2.31
Anisotropic B[1][2] -0.43
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.63
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.64
c_scbond_it 3.26
c_mcangle_it 3.28
c_mcbond_it 2.38
c_improper_angle_d 0.89
c_dihedral_angle_d 25.2
c_angle_deg 1.5
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3238
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 228

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHAKE-N-BAKE, SHARP, ARP/WARP Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
ARP/wARP model building
SHARP model building
SnB model building
HKL2000 data reduction
D*TREK data collection