X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 293.0
Details 10mM HEPES-KOH, 10mM MgCl2, 60mM NH4Cl, 6mM beta-mercaptoethanol, 11-12% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 411.79 α = 90
b = 411.79 β = 90
c = 173.16 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 225 mm Dynamically bendable mirror 2005-10-01
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.98010 SLS X06SA

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
3.3 148.83 97.1 0.162 -- -- 6.5 221305 214963 -- -3.0 87.687
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)
3.3 3.48 95.2 0.755 -- 2.5 6.2 30666

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 3.3 148.83 -- 0.0 -- 214953 10897 97.0 -- -- 0.259 0.301 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 3.3 3.42 20656 1014 19642 0.44 0.435 0.014 94.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 104.6
Anisotropic B[1][1] 15.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 15.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -31.65
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.012
c_dihedral_angle_d 19.9
c_improper_angle_d 1.78
c_angle_deg 1.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.53
Luzzati Sigma A (Observed) 1.01
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.6
Luzzati Sigma A (R-Free Set) 1.03
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19082
Nucleic Acid Atoms 32811
Heterogen Atoms 2
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
MOLREP phasing
CNS refinement version: 1.1
PDB_EXTRACT data extraction version: 2.000
XDS data scaling
XDS data reduction