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_gen_planes_other 0.003
r_gen_planes_refined 0.007
r_chiral_restr 0.045
r_dihedral_angle_4_deg 18.507
r_dihedral_angle_3_deg 12.165
r_dihedral_angle_2_deg 32.903
r_dihedral_angle_1_deg 6.637
r_angle_other_deg 0.872
r_angle_refined_deg 1.479
r_bond_other_d 0.003
r_bond_refined_d 0.011
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.7.0029 refinement
Xscale version: March 15, 2012 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation