X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.2
Temperature 298.0
Details PEG 200, sodium citrate, N,N-dimethylglycine, pH 5.20, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.7 α = 90
b = 90.84 β = 122.28
c = 88.4 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Bent conical Si-mirror (Rh coating) 2001-11-26
Diffraction Radiation
Monochromator Protocol
Bent Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 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
2.05 100 99.8 0.057 0.057 -- 2.88 45962 45962 0.0 0.0 38.9
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)
2.05 2.12 100.0 0.289 0.289 2.46 2.37 4569

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 2.05 10.0 0.0 0.0 45626 45584 2317 99.9 0.236 0.236 0.226 0.255 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 2.05 2.14 5670 278 5392 0.296 0.337 0.02 99.6
X Ray Diffraction 2.14 2.25 5666 299 5367 0.285 0.327 0.019 99.7
X Ray Diffraction 2.25 2.39 5692 265 5427 0.268 0.314 0.019 99.9
X Ray Diffraction 2.39 2.58 5691 303 5388 0.252 0.294 0.017 100.0
X Ray Diffraction 2.58 2.83 5709 302 5407 0.231 0.26 0.015 99.9
X Ray Diffraction 2.83 3.23 5695 302 5393 0.223 0.241 0.014 100.0
X Ray Diffraction 3.23 4.02 5705 282 5423 0.202 0.232 0.014 100.0
X Ray Diffraction 4.02 10.0 5756 286 5470 0.204 0.23 0.014 99.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 43.12
Anisotropic B[1][1] -2.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.86
Anisotropic B[2][2] -6.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.33
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.49
x_scbond_it 1.8
x_mcangle_it 1.85
x_mcbond_it 1.17
x_torsion_impr_deg 0.99
x_torsion_deg 23.1
x_angle_deg 1.4
x_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5337
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 431

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS 1.1 Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.1 refinement