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 pH 3.5, 1 mM Ac2Cu, Counter-diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.61 α = 90
b = 101.61 β = 90
c = 38.66 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 2005-12-20
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
2.4 50.8 99.5 -- 0.048 -- 10.25 9093 9093 -- -- 35.742
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 93.4 -- 0.3529 3.45 2.9 492

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 50.8 -- -- 9093 8566 408 93.915 0.188 0.188 0.1864 0.2295 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 -- 24 497 0.232 0.297 -- 78.701
X Ray Diffraction 2.462 2.53 -- 22 521 0.205 0.29 -- 84.579
X Ray Diffraction 2.53 2.603 -- 27 529 0.226 0.326 -- 87.284
X Ray Diffraction 2.603 2.683 -- 23 525 0.199 0.21 -- 92.101
X Ray Diffraction 2.683 2.77 -- 26 532 0.21 0.338 -- 92.079
X Ray Diffraction 2.77 2.867 -- 25 529 0.22 0.334 -- 95.848
X Ray Diffraction 2.867 2.975 -- 25 510 0.208 0.234 -- 95.365
X Ray Diffraction 2.975 3.096 -- 29 490 0.196 0.27 -- 97.191
X Ray Diffraction 3.096 3.233 -- 23 483 0.176 0.204 -- 98.062
X Ray Diffraction 3.233 3.39 -- 29 458 0.179 0.236 -- 98.185
X Ray Diffraction 3.39 3.573 -- 26 429 0.171 0.238 -- 97.639
X Ray Diffraction 3.573 3.789 -- 16 424 0.169 0.174 -- 98.434
X Ray Diffraction 3.789 4.049 -- 19 400 0.157 0.153 -- 99.054
X Ray Diffraction 4.049 4.371 -- 22 367 0.146 0.215 -- 98.731
X Ray Diffraction 4.371 4.784 -- 14 343 0.152 0.179 -- 99.167
X Ray Diffraction 4.784 5.343 -- 12 321 0.172 0.245 -- 99.107
X Ray Diffraction 5.343 6.158 -- 17 272 0.196 0.176 -- 100.0
X Ray Diffraction 6.158 7.515 -- 10 249 0.229 0.215 -- 100.0
X Ray Diffraction 7.515 10.513 -- 12 183 0.167 0.172 -- 100.0
X Ray Diffraction 10.513 50.8 -- 7 96 0.299 0.19 -- 82.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.717
Anisotropic B[1][1] -1.442
Anisotropic B[1][2] -0.721
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.442
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.163
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.226
r_symmetry_hbond_refined 0.172
r_dihedral_angle_4_deg 17.32
r_dihedral_angle_2_deg 34.261
r_nbd_refined 0.195
r_dihedral_angle_1_deg 5.665
r_scbond_it 0.897
r_scangle_it 1.478
r_nbtor_refined 0.3
r_xyhbond_nbd_refined 0.119
r_chiral_restr 0.072
r_mcangle_it 0.665
r_mcbond_it 0.369
r_gen_planes_refined 0.003
r_angle_refined_deg 1.228
r_dihedral_angle_3_deg 15.116
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1622
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 88

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