X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 10% PEG 3350, 10mM magnesium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 15% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.67 α = 90
b = 56.91 β = 106.53
c = 60.66 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-03-20
CCD MARMOSAIC 300 mm CCD -- 2009-03-20
Diffraction Radiation
Monochromator Protocol
Si(220) SINGLE WAVELENGTH
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.9794, 0.9796, 0.9719 APS 23-ID-D
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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
1.6 50 97.3 0.097 -- -- 4.4 39566 39268 -- 1.48 --

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
MAD 1.6 41.67 -- 0.0 -- 39268 1972 97.47 -- 0.209 0.207 0.252 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 1.6 1.642 -- 120 2302 0.333 0.367 -- 83.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.823
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.36
r_angle_refined_deg 1.731
r_mcbond_it 1.474
r_nbd_refined 0.212
r_dihedral_angle_4_deg 22.493
r_nbtor_refined 0.312
r_scangle_it 4.817
r_dihedral_angle_3_deg 14.962
r_symmetry_hbond_refined 0.22
r_dihedral_angle_2_deg 36.233
r_dihedral_angle_1_deg 7.632
r_bond_refined_d 0.015
r_chiral_restr 0.125
r_scbond_it 3.087
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.249
r_xyhbond_nbd_refined 0.169
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2038
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 153

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.13
RESOLVE phasing version: 2.13
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005