X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 297.0
Details 50 mM sodium succinate buffer, 200 mM sodium chloride, 30-35% methyl-pentane diol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.8 α = 90
b = 42.8 β = 90
c = 169.38 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors --
Diffraction Radiation
Monochromator Protocol
Si [111], horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8457 EMBL/DESY, Hamburg BW7B

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
1.78 20 99.1 -- 0.068 -- 7.45 28229 28229 -- -3.0 41.2
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)
1.78 1.89 95.6 -- 0.74 2.3 6.84 4348

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 1.88 20.0 -- -- 23345 23345 1225 99.77 -- 0.20152 0.20048 0.22221 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 1.88 1.929 29721 96 1688 0.272 0.291 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.067
Anisotropic B[1][1] 0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.25
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.138
r_xyhbond_nbd_refined 0.204
r_dihedral_angle_4_deg 15.038
r_mcangle_it 3.096
r_angle_refined_deg 1.938
r_nbtor_refined 0.318
r_symmetry_hbond_refined 0.238
r_dihedral_angle_1_deg 7.84
r_symmetry_vdw_refined 0.283
r_dihedral_angle_3_deg 15.143
r_mcbond_it 2.17
r_gen_planes_refined 0.009
r_dihedral_angle_2_deg 32.792
r_scangle_it 7.069
r_bond_refined_d 0.021
r_nbd_refined 0.244
r_scbond_it 4.471
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1770
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 111

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
XDS data reduction
XSCALE data scaling
MOLREP phasing