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 = 174.11 α = 90
b = 174.11 β = 90
c = 99.26 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 I02 -- DIAMOND I02

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
2.97 60.04 99.3 0.06 -- -- 3.63 -- 20202 -- -- --
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)
3.1 3.27 99.5 0.59 -- 1.29 3.68 --

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 3.1 37.428 -- -- -- 20201 1024 99.292 -- 0.18 0.1777 0.2213 --
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 3.1 3.18 -- 82 1393 0.326 0.429 -- 99.595
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 110.632
Anisotropic B[1][1] -4.036
Anisotropic B[1][2] -4.036
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.036
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.093
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 12.045
r_scbond_it 7.943
r_mcangle_it 13.678
r_mcbond_other 1.688
r_mcbond_it 6.644
r_nbd_refined 0.355
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.073
r_dihedral_angle_4_deg 16.85
r_dihedral_angle_3_deg 15.486
r_dihedral_angle_2_deg 33.551
r_dihedral_angle_1_deg 4.964
r_angle_other_deg 0.625
r_angle_refined_deg 1.125
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_nbd_other 0.193
r_nbtor_refined 0.207
r_xyhbond_nbd_refined 0.222
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4562
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 8

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