X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 20mM MGAC2, 13% MPD, PH 6.8, 100mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.42 α = 90
b = 299.95 β = 113.18
c = 145.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-10-26
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 1.0 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
2.8 20 96.2 0.078 -- -- 3.0 264104 254162 2.0 2.0 --
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)
2.8 2.9 97.1 0.491 -- 2.3 -- --

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 2.8 15.0 2.0 -- 254162 241453 12709 96.36 0.183 0.17997 0.17899 0.19857 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 2.8 2.87 -- 920 17465 0.315 0.342 -- 97.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.06
Anisotropic B[1][1] 2.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] -6.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.15
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_other 2.643
r_scbond_other 2.505
r_long_range_B_refined 2.984
r_sphericity_free 30.719
r_scangle_other 2.544
r_mcbond_other 2.245
r_mcangle_it 2.643
r_angle_other_deg 0.763
r_long_range_B_other 2.973
r_dihedral_angle_2_deg 36.863
r_chiral_restr 0.062
r_scbond_it 2.505
r_sphericity_bonded 5.401
r_dihedral_angle_3_deg 18.464
r_bond_other_d 0.002
r_angle_refined_deg 1.099
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 6.613
r_rigid_bond_restr 2.207
r_dihedral_angle_4_deg 18.907
r_mcbond_it 2.245
r_gen_planes_other 0.001
r_bond_refined_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49296
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 189

Software

Software
Software Name Purpose
REFMAC refinement
XDS data reduction
XSCALE data scaling
REFMAC phasing