X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.2
Details CRYSTALS WERE GROWN AT 4C USING 10-16% PEG 1000, 100MM NAK-PHOSPHATE PH 6.2, 500MM NACL, 4MM TCEP AS THE PRECIPITANT SOLUTION. THEY WERE SUBSEQUENTLY SOAKED IN THE PRESENCE OF COMPOUND.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 174.18 α = 90
b = 174.18 β = 90
c = 98.3 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 -- DIAMOND I03

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
2.96 87.09 99.9 0.07 -- -- 5.24 -- 23220 -- -- --
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)
2.96 3.12 99.9 0.58 -- 1.33 5.39 --

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
OTHER 2.958 87.092 -- -- -- 23216 1172 99.923 -- 0.169 0.1667 0.2097 --
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 2.958 3.035 -- 88 1644 0.282 0.318 -- 99.942
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 84.875
Anisotropic B[1][1] -0.472
Anisotropic B[1][2] -0.472
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.472
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.531
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 13.32
r_scbond_it 14.525
r_mcangle_it 11.347
r_mcbond_it 7.45
r_nbd_refined 0.28
r_gen_planes_refined 0.009
r_chiral_restr 0.113
r_dihedral_angle_4_deg 15.869
r_dihedral_angle_3_deg 16.545
r_dihedral_angle_2_deg 35.289
r_dihedral_angle_1_deg 5.741
r_angle_refined_deg 1.566
r_bond_refined_d 0.011
r_nbtor_refined 0.345
r_xyhbond_nbd_refined 0.257
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4559
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 13

Software

Computing
Computing Package Purpose
PHENIX Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
PHENIX model building