X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.76 α = 90
b = 109.62 β = 90
c = 138.65 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2007-04-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.9770 CHESS A1

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
1.38 20 98.5 0.06 -- -- 6.4 214738 211715 0.0 0.0 18.0
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)
1.38 1.4 82.0 0.33 -- 3.5 2.3 3723

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 1.38 19.81 -- 0.0 214738 210432 3138 97.99 -- 0.18 0.18 0.204 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 1.38 1.416 -- 196 12978 0.277 0.274 -- 83.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.616
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.206
r_scangle_it 3.72
r_xyhbond_nbd_refined 0.152
r_dihedral_angle_1_deg 6.08
r_angle_refined_deg 1.544
r_dihedral_angle_4_deg 18.041
r_chiral_restr 0.103
r_nbtor_refined 0.316
r_scbond_it 2.411
r_dihedral_angle_2_deg 36.699
r_bond_refined_d 0.014
r_symmetry_hbond_refined 0.156
r_mcbond_it 1.044
r_mcangle_it 1.68
r_dihedral_angle_3_deg 12.552
r_symmetry_vdw_refined 0.227
r_metal_ion_refined 0.038
r_gen_planes_refined 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8196
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 1470

Software

Software
Software Name Purpose
SAINT data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
SADABS data scaling
CNS phasing