X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 1.00M lithium chloride, 20.00% polyethylene glycol 6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71 α = 90
b = 71 β = 90
c = 184.7 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-05-23
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97891,0.97852 SSRL BL11-1

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
1.42 29.75 99.3 0.064 -- -- -- -- 88866 -- -3.0 23.315
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)
1.43 1.48 99.3 0.926 -- 1.4 -- --

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 1.42 29.753 -- 0.0 -- 88746 4451 99.45 -- 0.1446 0.1433 0.1684 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 1.424 1.46 -- 298 5948 0.249 0.302 -- 96.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.0331
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.29
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 5.202
r_mcbond_other 1.3
r_mcbond_it 1.997
r_mcangle_it 2.975
r_rigid_bond_restr 1.531
r_gen_planes_refined 0.006
r_angle_refined_deg 1.232
r_scbond_it 4.064
r_sphericity_free 5.991
r_angle_other_deg 0.876
r_dihedral_angle_3_deg 11.572
r_scangle_it 5.911
r_dihedral_angle_2_deg 34.714
r_dihedral_angle_4_deg 10.421
r_sphericity_bonded 3.634
r_bond_refined_d 0.01
r_chiral_restr 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3636
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 550

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: July 4, 2012
REFMAC refinement version: 5.5.0110
XDS data reduction
SHELXD phasing