X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 16-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6, 25 mM NaCl

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.07 α = 90
b = 113.32 β = 90
c = 174.64 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 MARMOSAIC 300 mm CCD -- 2009-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1

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
2.1 95.06 99.4 0.094 -- -- 4.2 -- 115660 -- -- --
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)
2.099 2.21 96.9 0.372 -- -- 3.8 16250

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 2.1 20.0 -- 0.0 -- 109936 5724 99.38 -- 0.1542 0.1524 0.1873 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 2.099 2.154 -- 398 7852 0.233 0.286 -- 97.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.962
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.01
r_bond_refined_d 0.025
r_mcbond_other 1.965
r_angle_refined_deg 2.029
r_mcbond_it 1.969
r_dihedral_angle_4_deg 14.999
r_chiral_restr 0.138
r_dihedral_angle_1_deg 6.083
r_mcangle_it 2.955
r_bond_other_d 0.002
r_dihedral_angle_3_deg 14.171
r_gen_planes_refined 0.013
r_dihedral_angle_2_deg 35.155
r_angle_other_deg 1.229
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11010
Nucleic Acid Atoms 0
Heterogen Atoms 144
Solvent Atoms 1170

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0151
PDB_EXTRACT data extraction version: 3.20
MOSFLM data reduction
SCALA data scaling
MOLREP phasing