X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 12-18% PEG4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE, 10MM DTT

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.91 α = 90
b = 88.91 β = 90
c = 104.64 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU CONFOCAL MULTILAYER OPTICS --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU3HR -- -- --

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
2.5 76 95.9 0.172 -- -- 1.8 -- 16237 -- -- --
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)
2.5 2.59 99.3 0.37 -- 1.9 1.85 --

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
MOLECULAR REPLACEMENT 2.5 76.7 -- -- -- 15415 820 95.9 -- 0.2 0.196 0.27 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 2.5 2.56 -- 71 1073 0.277 0.341 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.84
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.17
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.51
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.256
r_symmetry_hbond_refined 0.285
r_symmetry_vdw_other 0.255
r_scbond_it 3.917
r_gen_planes_other 0.003
r_nbd_refined 0.208
r_angle_refined_deg 1.666
r_chiral_restr 0.086
r_scangle_it 5.875
r_mcbond_it 3.117
r_bond_other_d 0.002
r_bond_refined_d 0.017
r_angle_other_deg 0.857
r_dihedral_angle_1_deg 7.479
r_mcangle_it 4.666
r_nbd_other 0.246
r_xyhbond_nbd_refined 0.2
r_nbtor_other 0.093
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2291
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 184

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.29 Structure Refinement
Software
Software Name Purpose
AMORE model building
REFMAC version: 5.1.29 refinement