X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 310.0
Details MPD, Cacodylate, KCl, MgCl2, spermine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.33 α = 90
b = 59.33 β = 90
c = 63.68 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.26 EMBL/DESY, HAMBURG BW7A

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
1.85 15 98.9 -- 0.052 -- 4.9 21273 21043 0.0 0.0 22.7
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)
1.85 1.9 98.7 -- 0.188 -- -- --

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
MAD 1.85 8.0 -- 2.0 21156 19553 1476 92.4 -- 0.218 0.218 0.219 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 1.85 1.96 -- 193 2511 0.279 0.284 0.02 77.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.5
Anisotropic B[1][1] -3.12
Anisotropic B[1][2] 0.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.23
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.76
c_dihedral_angle_d 9.1
c_angle_deg 1.6
c_bond_d 0.014
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 10.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 980
Heterogen Atoms 6
Solvent Atoms 283

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS 0.4 Structure Refinement
Software
Software Name Purpose
CNS version: 0.4 refinement