X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 293.0
Details PEG4000, sodium chloride, HEPES, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.89 α = 90
b = 84.94 β = 90
c = 249.25 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 4 -- 2000-12-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.000 APS 14-BM-C

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
2.49 49.88 93.5 0.074 -- -- 5.0 53049 49606 0.0 -2.0 42.5
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)
2.5 2.59 81.7 0.441 -- 2.0 2.0 4223

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 2.5 49.88 -- 0.0 53069 49423 2636 93.1 0.243 0.243 0.209 0.245 same set of reflections as used in refining the native lambda3 structure
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 2.5 2.61 5226 155 5071 0.286 0.285 0.023 80.1
X Ray Diffraction 2.61 2.75 5723 231 5492 0.245 0.244 0.016 87.1
X Ray Diffraction 2.75 2.92 5955 272 5683 0.233 0.232 0.014 90.6
X Ray Diffraction 2.92 3.15 6044 362 5682 0.224 0.224 0.012 92.1
X Ray Diffraction 3.15 3.47 6253 405 5848 0.207 0.207 0.01 94.9
X Ray Diffraction 3.47 3.97 6577 412 6165 0.197 0.198 0.01 99.0
X Ray Diffraction 3.97 5.0 6701 394 6307 0.169 0.17 0.009 100.0
X Ray Diffraction 5.0 49.88 6944 405 6539 0.219 0.218 0.011 99.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 33.69
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 1.1
x_torsion_deg 22.2
x_angle_deg 1.5
x_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9929
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 671

Software

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