X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 30.0% polyethylene glycol 4000, 0.2M magnesium chloride, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.75 α = 91.64
b = 65.32 β = 92.35
c = 78.76 γ = 104.5
Symmetry
Space Group P 1

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) 2012-08-02
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- 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
1.87 48.32 87.2 0.059 -- -- -- -- 53817 -- -3.0 30.595
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)
1.87 1.94 61.5 0.57 -- 1.8 -- --

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
SAD 1.87 48.317 -- 0.0 -- 53272 2703 86.62 -- 0.1984 0.1963 0.2382 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 1.872 1.921 -- 91 2185 0.449 0.489 -- 49.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.5108
Anisotropic B[1][1] -0.56
Anisotropic B[1][2] 0.85
Anisotropic B[1][3] -0.47
Anisotropic B[2][2] 3.15
Anisotropic B[2][3] 0.1
Anisotropic B[3][3] -3.19
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.045
r_angle_other_deg 0.872
r_gen_planes_other 0.003
r_bond_refined_d 0.011
r_dihedral_angle_4_deg 18.507
r_angle_refined_deg 1.479
r_dihedral_angle_2_deg 32.903
r_dihedral_angle_3_deg 12.165
r_bond_other_d 0.003
r_dihedral_angle_1_deg 6.637
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4836
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 393

Software

Software
Software Name Purpose
MOLPROBITY validation version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: March 15, 2012
REFMAC refinement version: 5.7.0029
XDS data reduction
SHELXD phasing