X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 28.63 α = 90
b = 53.57 β = 98.31
c = 72.2 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 KOHZU double crystal monochromator 2000-08-06
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 1.05 NSLS X4A

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
1.79 19.68 90.1 0.073 0.073 -- 6.81 20226 18075 0.0 0.0 14.8
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)
1.8 1.83 90.5 0.18 0.18 6.2 2.1 894

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 1.8 19.68 0.0 0.0 20134 17518 1369 87.0 0.227 0.227 0.189 0.228 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 1.8 1.88 -- 163 1880 0.243 0.2714 0.019 82.3
X Ray Diffraction 1.88 1.98 -- 156 1957 0.232 0.2871 0.019 84.0
X Ray Diffraction 1.98 2.1 -- 167 1936 0.217 0.2707 0.017 84.1
X Ray Diffraction 2.1 2.27 -- 167 1938 0.194 0.2507 0.015 84.1
X Ray Diffraction 2.27 2.5 -- 176 1948 0.187 0.2397 0.014 84.8
X Ray Diffraction 2.5 2.86 -- 166 2130 0.194 0.262 0.015 90.1
X Ray Diffraction 2.86 3.59 -- 178 2203 0.168 0.21 0.013 94.1
X Ray Diffraction 3.59 19.68 -- 196 2157 0.175 0.1901 0.013 91.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 25.29
Anisotropic B[1][1] 15.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.85
Anisotropic B[2][2] -7.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.27
RMS Deviations
Key Refinement Restraint Deviation
x_scbond_it 2.09
x_mcangle_it 1.84
x_torsion_impr_deg 4.3
x_dihedral_angle_d 26.4
x_angle_deg 2.5
x_improper_angle_d 4.3
x_mcbond_it 1.27
x_bond_d 0.016
x_torsion_deg 26.4
x_scangle_it 3.14
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1736
Nucleic Acid Atoms 160
Heterogen Atoms 0
Solvent Atoms 323

Software

Software
Software Name Purpose
CNS refinement version: 1.0
ADSC data collection
SCALEPACK data scaling
CNS phasing