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, HEPES 15 mM pH 4.1, Ac2Cu 1mM, AcNa 15m, pH 3.5, Counter-diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.17 α = 90
b = 103.17 β = 90
c = 41.83 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 2006-02-20
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
2.25 51.58 99.9 -- 0.0241 -- 28.93 12308 12308 -- -- 37.35
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)
2.25 2.3 100.0 -- 0.1501 6.46 22.28 779

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 2.25 51.58 -- -- 12308 12106 1186 98.447 0.202 0.202 0.1954 0.268 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 2.25 2.308 -- 66 799 0.235 0.314 -- 96.973
X Ray Diffraction 2.308 2.372 -- 78 813 0.223 0.257 -- 99.331
X Ray Diffraction 2.372 2.44 -- 67 742 0.23 0.336 -- 96.77
X Ray Diffraction 2.44 2.515 -- 105 708 0.226 0.359 -- 98.188
X Ray Diffraction 2.515 2.597 -- 86 710 0.224 0.309 -- 98.15
X Ray Diffraction 2.597 2.688 -- 77 675 0.212 0.298 -- 98.301
X Ray Diffraction 2.688 2.789 -- 78 684 0.204 0.308 -- 98.323
X Ray Diffraction 2.789 2.903 -- 56 630 0.214 0.4 -- 97.721
X Ray Diffraction 2.903 3.032 -- 73 614 0.223 0.296 -- 98.424
X Ray Diffraction 3.032 3.179 -- 68 599 0.19 0.267 -- 98.815
X Ray Diffraction 3.179 3.35 -- 58 554 0.187 0.276 -- 99.029
X Ray Diffraction 3.35 3.553 -- 59 541 0.189 0.265 -- 99.01
X Ray Diffraction 3.553 3.797 -- 62 505 0.167 0.206 -- 99.299
X Ray Diffraction 3.797 4.099 -- 56 468 0.16 0.197 -- 99.431
X Ray Diffraction 4.099 4.487 -- 51 443 0.164 0.224 -- 100.0
X Ray Diffraction 4.487 5.012 -- 38 398 0.164 0.217 -- 100.0
X Ray Diffraction 5.012 5.779 -- 41 361 0.197 0.266 -- 100.0
X Ray Diffraction 5.779 7.055 -- 29 311 0.222 0.257 -- 100.0
X Ray Diffraction 7.055 9.886 -- 25 234 0.186 0.25 -- 99.615
X Ray Diffraction 9.886 51.58 -- 13 131 0.258 0.471 -- 87.805
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.62
Anisotropic B[1][1] -2.082
Anisotropic B[1][2] -1.041
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.082
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.123
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.798
r_scangle_it 1.648
r_dihedral_angle_4_deg 24.691
r_dihedral_angle_1_deg 5.783
r_symmetry_hbond_refined 0.232
r_bond_refined_d 0.014
r_angle_refined_deg 1.403
r_scbond_it 1.134
r_symmetry_vdw_refined 0.183
r_nbtor_refined 0.306
r_mcbond_it 1.232
r_dihedral_angle_2_deg 36.268
r_gen_planes_refined 0.005
r_mcangle_it 1.832
r_nbd_refined 0.207
r_xyhbond_nbd_refined 0.397
r_chiral_restr 0.087
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1640
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 99

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