X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 290.0
Details 100 mM MES, pH 6.5, NaBr or NaCl, 8 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.17 α = 90
b = 84.9 β = 90
c = 124.28 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-05-31
CCD MARRESEARCH -- 1999-10-26
Diffraction Radiation
Monochromator Protocol
-- MAD
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C -- NSLS X8C
SYNCHROTRON NSLS BEAMLINE X26C -- NSLS X26C

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
1.9 50 99.2 0.087 -- -- 9.28 36016 35804 -- -3.0 17.6
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)
1.9 1.97 96.4 0.418 -- 4.35 6.05 3500

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 1.9 25.0 0.0 0.0 33605 33605 1668 93.3 -- -- 0.241 0.271 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 1.9 1.97 -- 149 2621 0.301 0.337 0.028 78.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.4
Anisotropic B[1][1] 2.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -13.397
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.837
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.75
c_scbond_it 1.787
c_mcangle_it 2.07
c_mcbond_it 1.226
c_improper_angle_d 0.93
c_dihedral_angle_d 22.8
c_angle_deg 1.61
c_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2349
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 100

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE, SHARP Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
SHARP model building
SNB model building