X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY SOAKED IN THE SOLUTION. AFTER A FEW DAYS AT 4C, SMALL HEXAGONAL BIPYRAMIDS STARTED STARTED TO APPEAR AND REACHED THEIR MAXIMUM SIZE AFTER ONE WEEK. THE BEST CRYOCRYSTALLOGRAPHY CONDITIONS WERE OBTAINED BY SOAKING THESE CRYSTALS IN A CRYSTALLIZATION SOLUTION CONTAINING 7.5% MPD, pH 7.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 220.39 α = 90
b = 220.39 β = 90
c = 102.64 γ = 120
Symmetry
Space Group P 62

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4r MIRRORS 2001-06-15
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

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 25 91.3 0.064 -- -- 6.5 -- 89606 -- -- --
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 84.0 0.354 -- 3.0 -- --

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 2.51 30.0 -- -- -- 85075 4494 92.1 -- 0.195 0.192 0.258 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 2.51 2.59 -- 446 8239 0.226 0.317 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.61
Anisotropic B[1][1] 1.57
Anisotropic B[1][2] 0.79
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.36
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.751
r_symmetry_vdw_refined 0.2
r_scbond_it 1.647
r_xyhbond_nbd_refined 0.152
r_nbd_refined 0.222
r_symmetry_hbond_refined 0.214
r_gen_planes_refined 0.005
r_chiral_restr 0.099
r_mcbond_it 0.515
r_angle_refined_deg 1.547
r_mcangle_it 0.97
r_bond_refined_d 0.014
r_scangle_it 2.385
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15038
Nucleic Acid Atoms 0
Heterogen Atoms 2752
Solvent Atoms 497

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling