X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Counter Diffusion
pH 3.5
Temperature 277.0
Details 60% (v/v) MPD, AcNa 15 mM pH3.5, Ac2Cu 1 mM, Counter-diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.5 α = 90
b = 103.5 β = 90
c = 41.78 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
2.4 44.82 99.7 -- 0.0242 -- 10.9 10198 10198 -- -- 49.79
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)
2.4 2.45 97.9 -- 0.2876 4.36 5.89 605

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 2.4 44.82 -- -- 10198 10162 1014 99.471 0.206 0.206 0.2007 0.2575 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 2.4 2.462 -- 82 663 0.238 0.376 -- 97.641
X Ray Diffraction 2.462 2.529 -- 72 642 0.242 0.392 -- 100.0
X Ray Diffraction 2.529 2.603 -- 76 645 0.246 0.383 -- 99.723
X Ray Diffraction 2.603 2.682 -- 69 578 0.22 0.31 -- 99.233
X Ray Diffraction 2.682 2.77 -- 77 613 0.25 0.305 -- 100.0
X Ray Diffraction 2.77 2.867 -- 67 569 0.225 0.363 -- 99.843
X Ray Diffraction 2.867 2.975 -- 60 562 0.24 0.347 -- 100.0
X Ray Diffraction 2.975 3.095 -- 52 546 0.205 0.264 -- 100.0
X Ray Diffraction 3.095 3.232 -- 62 523 0.19 0.224 -- 99.829
X Ray Diffraction 3.232 3.389 -- 62 484 0.2 0.231 -- 100.0
X Ray Diffraction 3.389 3.571 -- 50 477 0.188 0.215 -- 99.811
X Ray Diffraction 3.571 3.787 -- 55 444 0.174 0.251 -- 99.402
X Ray Diffraction 3.787 4.046 -- 39 417 0.172 0.237 -- 99.563
X Ray Diffraction 4.046 4.367 -- 40 410 0.157 0.178 -- 100.0
X Ray Diffraction 4.367 4.779 -- 42 359 0.148 0.237 -- 100.0
X Ray Diffraction 4.779 5.336 -- 26 351 0.181 0.249 -- 100.0
X Ray Diffraction 5.336 6.147 -- 31 294 0.234 0.254 -- 100.0
X Ray Diffraction 6.147 7.493 -- 28 254 0.23 0.252 -- 100.0
X Ray Diffraction 7.493 10.452 -- 17 207 0.185 0.17 -- 99.556
X Ray Diffraction 10.452 44.82 -- 7 110 0.338 0.179 -- 85.401
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.845
Anisotropic B[1][1] -2.785
Anisotropic B[1][2] -1.392
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.785
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.177
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.27
r_angle_refined_deg 1.597
r_bond_refined_d 0.029
r_nbd_refined 0.22
r_dihedral_angle_4_deg 4.366
r_symmetry_hbond_refined 0.161
r_scangle_it 1.789
r_xyhbond_nbd_refined 0.204
r_mcangle_it 1.93
r_chiral_restr 0.094
r_gen_planes_refined 0.005
r_symmetry_vdw_refined 0.214
r_scbond_it 1.226
r_dihedral_angle_1_deg 6.908
r_nbtor_refined 0.304
r_dihedral_angle_3_deg 16.221
r_dihedral_angle_2_deg 36.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 60

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