X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Counter Diffusion
pH 7
Temperature 277.0
Details 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counter-diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.99 α = 90
b = 102.99 β = 90
c = 42.44 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER SMART 6000 Montel Optics --
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER 1.5418 -- --

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
2.45 44.6 99.9 -- 0.0319 -- 9.43 9672 9672 -- -- 49.495
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)
2.45 2.5 100.0 -- 0.2322 3.93 8.26 574

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 2.45 44.6 -- -- 9672 9589 462 99.275 0.212 0.212 0.2088 0.278 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 2.45 2.514 -- 50 667 0.241 0.341 -- 100.0
X Ray Diffraction 2.514 2.582 -- 31 645 0.27 0.339 -- 100.0
X Ray Diffraction 2.582 2.657 -- 36 638 0.261 0.269 -- 100.0
X Ray Diffraction 2.657 2.738 -- 33 604 0.244 0.379 -- 100.0
X Ray Diffraction 2.738 2.828 -- 26 605 0.251 0.321 -- 99.842
X Ray Diffraction 2.828 2.927 -- 34 577 0.246 0.352 -- 99.674
X Ray Diffraction 2.927 3.036 -- 28 562 0.265 0.301 -- 98.333
X Ray Diffraction 3.036 3.16 -- 26 513 0.232 0.255 -- 99.263
X Ray Diffraction 3.16 3.3 -- 25 514 0.21 0.312 -- 97.822
X Ray Diffraction 3.3 3.46 -- 18 506 0.229 0.266 -- 99.242
X Ray Diffraction 3.46 3.646 -- 20 468 0.205 0.26 -- 98.387
X Ray Diffraction 3.646 3.865 -- 25 444 0.195 0.26 -- 98.529
X Ray Diffraction 3.865 4.13 -- 24 427 0.183 0.232 -- 99.339
X Ray Diffraction 4.13 4.458 -- 17 392 0.159 0.25 -- 99.272
X Ray Diffraction 4.458 4.878 -- 15 359 0.171 0.158 -- 100.0
X Ray Diffraction 4.878 5.446 -- 17 335 0.171 0.318 -- 100.0
X Ray Diffraction 5.446 6.273 -- 12 298 0.197 0.277 -- 100.0
X Ray Diffraction 6.273 7.645 -- 10 259 0.216 0.256 -- 100.0
X Ray Diffraction 7.645 10.656 -- 11 202 0.149 0.252 -- 99.533
X Ray Diffraction 10.656 44.6 -- 4 112 0.316 0.576 -- 88.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.1
Anisotropic B[1][1] -3.366
Anisotropic B[1][2] -1.683
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.366
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.049
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.731
r_chiral_restr 0.108
r_mcangle_it 1.929
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 16.752
r_xyhbond_nbd_refined 0.195
r_mcbond_it 1.265
r_dihedral_angle_4_deg 20.675
r_nbtor_refined 0.313
r_dihedral_angle_2_deg 41.677
r_scangle_it 1.976
r_dihedral_angle_1_deg 6.14
r_symmetry_hbond_refined 0.229
r_nbd_refined 0.243
r_scbond_it 1.415
r_symmetry_vdw_refined 0.21
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1645
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 79

Software

Software
Software Name Purpose
SAINT data scaling
MOLREP phasing
REFMAC refinement version: refmac_5.2.0019
PDB_EXTRACT data extraction version: 1.700
PROTEUM PLUS data reduction version: 2
SADABS data scaling
XPREP data reduction
Coot model building
MolProbity model building