X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details ROD-SHAPED CRYSTALS WERE GROWN BY SITTING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.1M SODIUM CACODYLATE, 0.02M IMIDAZOLE, PH 7.2, 10% PEG3350, AND 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.24 α = 90
b = 46.34 β = 101.76
c = 94.31 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-11-17
Diffraction Radiation
Monochromator Protocol
-- MULTIPLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B -- NSLS X9B

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
3 15 98.6 0.06 -- -- 3.4 -- 11250 -- 0.04 43.3
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)
3.0 3.11 96.5 0.177 -- 5.5 2.9 --

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 PHASING 3.1 15.0 -- 0.2 -- 10183 525 5.1 -- 0.256 0.256 0.337 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 3.1 3.21 -- 42 977 0.334 0.459 -- 96.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.0
Anisotropic B[1][1] 0.817
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -10.779
Anisotropic B[2][2] -3.077
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.26
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.97
c_bond_d 0.01
c_angle_deg 1.41
c_dihedral_angle_d 24.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.47
Luzzati Sigma A (Observed) 0.53
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.58
Luzzati Sigma A (R-Free Set) 0.7
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3397
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

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