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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.08 α = 90
b = 103.08 β = 90
c = 42.59 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 2005-06-18
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
2.2 51.54 99.9 -- 0.0258 -- 1.92 13343 13343 -- -- 38.183
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)
2.2 2.25 100.0 -- 0.1934 4.16 1.7 856

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 2.2 51.54 -- -- 13343 12846 1273 96.297 0.233 0.233 0.2269 0.2935 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 2.2 2.257 -- 94 863 0.316 0.36 -- 98.66
X Ray Diffraction 2.257 2.319 -- 95 831 0.319 0.41 -- 97.474
X Ray Diffraction 2.319 2.386 -- 90 797 0.324 0.351 -- 95.172
X Ray Diffraction 2.386 2.459 -- 83 770 0.284 0.309 -- 95.521
X Ray Diffraction 2.459 2.54 -- 77 751 0.313 0.33 -- 95.172
X Ray Diffraction 2.54 2.629 -- 79 724 0.295 0.368 -- 95.03
X Ray Diffraction 2.629 2.728 -- 77 704 0.28 0.374 -- 95.128
X Ray Diffraction 2.728 2.839 -- 90 662 0.288 0.322 -- 95.19
X Ray Diffraction 2.839 2.965 -- 72 630 0.281 0.397 -- 93.976
X Ray Diffraction 2.965 3.109 -- 63 625 0.237 0.314 -- 95.159
X Ray Diffraction 3.109 3.276 -- 57 607 0.231 0.23 -- 94.722
X Ray Diffraction 3.276 3.474 -- 68 543 0.211 0.346 -- 96.372
X Ray Diffraction 3.474 3.713 -- 68 536 0.197 0.263 -- 96.486
X Ray Diffraction 3.713 4.009 -- 51 506 0.178 0.302 -- 97.891
X Ray Diffraction 4.009 4.389 -- 65 457 0.165 0.246 -- 99.429
X Ray Diffraction 4.389 4.902 -- 44 430 0.174 0.169 -- 99.163
X Ray Diffraction 4.902 5.652 -- 33 396 0.178 0.348 -- 99.536
X Ray Diffraction 5.652 6.901 -- 34 337 0.212 0.293 -- 100.0
X Ray Diffraction 6.901 9.674 -- 17 269 0.177 0.204 -- 99.652
X Ray Diffraction 9.674 51.54 -- 16 135 0.296 0.201 -- 85.311
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.267
Anisotropic B[1][1] -4.208
Anisotropic B[1][2] -2.104
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.208
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.312
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.705
r_mcangle_it 1.869
r_nbtor_refined 0.299
r_symmetry_hbond_refined 0.202
r_nbd_refined 0.193
r_scangle_it 1.532
r_dihedral_angle_1_deg 5.775
r_dihedral_angle_4_deg 23.872
r_dihedral_angle_2_deg 37.791
r_chiral_restr 0.076
r_mcbond_it 1.179
r_gen_planes_refined 0.004
r_scbond_it 1.004
r_xyhbond_nbd_refined 0.157
r_angle_refined_deg 1.229
r_symmetry_vdw_refined 0.201
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1630
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