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 = 174.59 α = 90
b = 174.59 β = 90
c = 99.42 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 (QUANTUM 315R) ADSC -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
3.16 50.4 99.6 0.1 -- -- 3.61 -- 19246 -- -- --
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)
3.16 3.33 99.0 0.55 -- 1.41 3.53 --

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 3.162 38.668 -- -- -- 19245 973 99.535 -- 0.162 0.1594 0.2073 --
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 3.162 3.244 -- 80 1325 0.298 0.332 -- 97.978
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 101.642
Anisotropic B[1][1] -2.509
Anisotropic B[1][2] -2.509
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.509
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.138
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 11.827
r_scbond_it 13.112
r_mcangle_it 8.955
r_mcbond_it 6.308
r_nbd_refined 0.278
r_gen_planes_refined 0.008
r_chiral_restr 0.098
r_dihedral_angle_4_deg 20.364
r_dihedral_angle_3_deg 18.03
r_dihedral_angle_2_deg 32.825
r_dihedral_angle_1_deg 5.543
r_angle_refined_deg 1.379
r_bond_refined_d 0.01
r_nbtor_refined 0.359
r_xyhbond_nbd_refined 0.165
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4568
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 6

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