X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 291.0
Details 3.0 M NaCl, 100 mM Sodium acetate, 100 mM Li2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.92 α = 90
b = 96.95 β = 90
c = 104.89 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-08-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
2.4 50 96.5 0.192 0.192 -- 4.0 38830 23837 -- -- 10.7
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)
2.4 2.49 87.6 0.422 0.422 2.2 2.9 2120

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 2.4 35.47 0.0 0.0 23837 23837 3712 92.2 0.203 0.203 0.203 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 2.4 2.55 2120 462 4462 0.277 0.355 0.017 64.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.791
Anisotropic B[1][1] -7.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.59
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 22.5
c_improper_angle_d 0.89
c_bond_d 0.007
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4648
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 259

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement version: 1.2
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
SHELXD phasing