X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 280.0
Details 17 % PEG 4000, 100mM Hepes 8.5, 200mM Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 280K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.53 α = 90
b = 97.45 β = 93.1
c = 106.94 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 Double crystal 2006-07-14
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2

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
1.7 41.38 96.8 0.09 -- -- 6.19 170739 170738 0.0 0.0 --
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)
1.7 1.76 94.5 0.48 -- 2.9 6.03 16592

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 1.7 41.38 -- 0.0 170707 170707 8560 96.77 -- 0.183 0.181 0.234 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 1.7 1.744 12269 597 11672 0.272 0.347 -- 94.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.348
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.05
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.211
r_nbtor_refined 0.306
r_dihedral_angle_1_deg 5.562
r_scbond_it 2.619
r_chiral_restr 0.121
r_gen_planes_refined 0.008
r_angle_refined_deg 1.602
r_symmetry_hbond_refined 0.187
r_bond_refined_d 0.02
r_dihedral_angle_3_deg 14.959
r_symmetry_vdw_refined 0.182
r_scangle_it 3.921
r_dihedral_angle_2_deg 38.618
r_dihedral_angle_4_deg 15.864
r_mcbond_it 1.108
r_xyhbond_nbd_refined 0.166
r_mcangle_it 1.563
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11958
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 2228

Software

Software
Software Name Purpose
REFMAC refinement
CNS refinement
d*TREK data scaling version: 9.6LDz
PDB_EXTRACT data extraction version: 2.000
CNS phasing