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_angle_deg 1.4
x_bond_d 0.007
x_torsion_impr_deg 0.99
x_mcangle_it 1.85
x_torsion_deg 23.1
x_mcbond_it 1.17
x_scbond_it 1.8
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

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
CNS phasing version: 1.1