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, Ac2Cu 1 mM, 15mM Hepes pH 7.0, pH 3.5, Counter-diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.92 α = 90
b = 102.92 β = 90
c = 42.56 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 2005-12-23
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 51.46 99.9 -- 0.022 -- 21.63 12447 12447 -- -- 44.395
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 -- 0.2079 3.59 12.91 786

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 51.434 -- -- 12446 12038 1180 96.761 0.234 0.234 0.228 0.2901 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 -- 107 803 0.388 0.446 -- 99.562
X Ray Diffraction 2.308 2.372 -- 88 784 0.359 0.527 -- 97.758
X Ray Diffraction 2.372 2.44 -- 80 742 0.344 0.521 -- 96.14
X Ray Diffraction 2.44 2.515 -- 69 722 0.335 0.504 -- 94.391
X Ray Diffraction 2.515 2.597 -- 71 697 0.319 0.512 -- 94.233
X Ray Diffraction 2.597 2.688 -- 68 664 0.296 0.384 -- 94.087
X Ray Diffraction 2.688 2.789 -- 66 655 0.292 0.383 -- 93.88
X Ray Diffraction 2.789 2.903 -- 54 638 0.282 0.394 -- 96.379
X Ray Diffraction 2.903 3.032 -- 66 620 0.283 0.363 -- 94.231
X Ray Diffraction 3.032 3.179 -- 69 569 0.234 0.318 -- 96.52
X Ray Diffraction 3.179 3.35 -- 57 557 0.216 0.258 -- 97.46
X Ray Diffraction 3.35 3.553 -- 60 538 0.211 0.283 -- 97.236
X Ray Diffraction 3.553 3.797 -- 58 510 0.193 0.21 -- 98.44
X Ray Diffraction 3.797 4.099 -- 47 484 0.173 0.196 -- 99.438
X Ray Diffraction 4.099 4.487 -- 55 438 0.169 0.226 -- 99.798
X Ray Diffraction 4.487 5.012 -- 49 397 0.151 0.194 -- 99.554
X Ray Diffraction 5.012 5.779 -- 45 355 0.197 0.298 -- 100.0
X Ray Diffraction 5.779 7.055 -- 30 315 0.215 0.245 -- 99.711
X Ray Diffraction 7.055 9.885 -- 31 233 0.192 0.214 -- 99.623
X Ray Diffraction 9.885 51.434 -- 10 137 0.293 0.338 -- 89.091
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.103
Anisotropic B[1][1] -0.759
Anisotropic B[1][2] -0.379
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.759
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.138
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.725
r_symmetry_hbond_refined 0.221
r_mcbond_it 1.193
r_nbd_refined 0.2
r_scangle_it 1.619
r_xyhbond_nbd_refined 0.16
r_scbond_it 1.121
r_symmetry_vdw_refined 0.187
r_angle_refined_deg 1.303
r_dihedral_angle_2_deg 37.034
r_chiral_restr 0.079
r_gen_planes_refined 0.004
r_dihedral_angle_4_deg 12.176
r_mcangle_it 1.889
r_nbtor_refined 0.303
r_dihedral_angle_1_deg 6.213
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1627
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 97

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