X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 295.0
Details sodium-potassium phosphate buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.47 α = 90
b = 61.69 β = 90
c = 89.21 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 MARRESEARCH mirrors 2001-01-01
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 1.0000 APS 5ID-B

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
1.75 20 93.5 0.041 -- -- 5.0 22408 22408 0.0 -3.0 26.8
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)
1.75 1.81 93.3 0.225 -- 6.4 4.9 2202

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 1.75 19.0 0.0 0.0 -- 21771 2163 91.7 -- -- 0.186 0.22 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 1.75 1.81 2202 207 2202 0.2342 0.2838 -- 93.3
X Ray Diffraction 1.81 1.89 2208 208 -- 0.2016 0.2462 -- 93.8
X Ray Diffraction 1.89 1.97 2198 196 -- 0.1909 0.2339 -- 93.3
X Ray Diffraction 1.97 2.07 2181 223 -- 0.1859 0.2446 -- 92.2
X Ray Diffraction 2.07 2.2 2185 227 -- 0.1835 0.2289 -- 92.4
X Ray Diffraction 2.2 2.37 2210 222 -- 0.1659 0.2079 -- 93.6
X Ray Diffraction 2.37 2.61 2284 221 -- 0.1815 0.2172 -- 95.7
X Ray Diffraction 2.61 2.99 2332 219 -- 0.1898 0.2389 -- 96.0
X Ray Diffraction 2.99 3.76 2303 21 -- 0.1788 0.1922 -- 94.7
X Ray Diffraction 3.76 19.0 2305 229 -- 0.1876 0.2092 -- 89.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.5
Anisotropic B[1][1] 3.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.139
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.21
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.0
c_angle_deg 1.46
c_dihedral_angle_d 21.9
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2026
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 291

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.0