X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 293.0
Details 14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.2 α = 90
b = 99.2 β = 90
c = 78.9 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-06-01
Diffraction Radiation
Monochromator Protocol
SI 111 CHANNEL MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.000, 0.9796, 0.9789, 0.9599 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
2.8 20 98.3 -- 0.088 -- 13.4 11156 11156 0.0 -3.0 70.9
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)
2.8 2.97 97.9 -- 0.422 4.8 -- --

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 AND MOLECULAR REPLACEMENT 2.8 19.37 -- 0.0 10904 10904 569 96.0 -- -- 0.201 0.282 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 2.8 2.97 1564 91 1564 0.324 0.371 0.039 89.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 62.8
Anisotropic B[1][1] -14.22
Anisotropic B[1][2] 5.3
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -14.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 28.43
RMS Deviations
Key Refinement Restraint Deviation
o_scbond_it 1.8
o_mcbond_it 1.36
o_improper_angle_d 0.87
o_bond_d 0.008
o_angle_deg 1.4
o_mcangle_it 2.42
o_scangle_it 2.79
o_dihedral_angle_d 25.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3368
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 43

Software

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