X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 277.0
Details 2-methyl-2,4-pentanediol, MES buffer, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.01 α = 89.96
b = 53.41 β = 90
c = 63.26 γ = 91.78
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2001-05-19
Diffraction Radiation
Monochromator Protocol
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.964818 SSRL BL11-1

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
2.3 29.88 97.3 -- 0.043 -- 3.0 25724 25456 0.0 -- 20.0
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)
2.3 2.34 97.6 -- 0.106 -- 3.0 1270

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
MOLECULAR REPLACEMENT 2.3 29.88 -- 0.0 25456 25456 2513 97.3 -- 0.22 0.22 0.264 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 2.3 2.38 -- 222 2267 0.222 0.298 0.02 95.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.6
Anisotropic B[1][1] 5.37
Anisotropic B[1][2] -0.33
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.6
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.65
c_mcangle_it 1.86
c_mcbond_it 1.16
c_scbond_it 1.8
c_bond_d 0.006
c_angle_deg 1.1
c_scangle_it 2.6
c_dihedral_angle_d 22.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4019
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 188

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
CNS phasing version: 1.1