X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 303.0
Details 1,6-hexanediol, ammonium chloride, magnesium chloride, zinc acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.81 α = 90
b = 86.81 β = 90
c = 156.07 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2002-06-13
CCD MARRESEARCH mirrors 2002-05-23
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9793 SPRING-8 BL41XU
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9132 SPRING-8 BL41XU

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
1.95 50 98.7 0.071 0.071 -- 8.5 50210 49557 0.0 0.0 23.1
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)
1.95 1.98 93.1 0.282 0.282 2.2 2.9 2302

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
SAD 1.95 34.63 0.0 0.0 50210 49545 4982 98.6 -- 0.188 0.188 0.239 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 1.95 2.07 -- 807 7049 0.258 0.299 0.011 94.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 43.6
Anisotropic B[1][1] 3.86
Anisotropic B[1][2] 3.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.72
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 8.22
c_scbond_it 6.27
c_mcangle_it 5.07
c_mcbond_it 4.48
c_improper_angle_d 1.95
c_bond_d 0.026
c_angle_deg 2.2
c_dihedral_angle_d 21.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2414
Nucleic Acid Atoms 1578
Heterogen Atoms 17
Solvent Atoms 364

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement