X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.2M magnesium chloride, 2.5M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.57 α = 90
b = 96.57 β = 90
c = 148.97 γ = 90
Symmetry
Space Group P 43 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) 2014-05-21
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 0.91837,0.97941,0.97898 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
2.3 25.2 98.5 -- 0.185 -- 8.8 31486 31486 -- -- --
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)
2.3 2.36 99.6 -- 1.256 1.8 9.1 2303

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 2.3 25.203 -- 0.0 -- 31457 1512 98.25 -- 0.1617 0.1589 0.213 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 2.3 2.36 -- 45 2250 0.226 0.259 -- 99.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.6185
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.317
r_dihedral_angle_3_deg 14.128
r_chiral_restr 0.094
r_mcangle_it 6.32
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcbond_other 4.943
r_angle_refined_deg 1.618
r_mcbond_it 4.988
r_dihedral_angle_4_deg 18.847
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_angle_other_deg 0.794
r_dihedral_angle_1_deg 6.645
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3225
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 277

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SOLVE phasing
SCALA data scaling version: 3.3.20
REFMAC refinement version: 5.7.0032
MOSFLM data reduction