X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.1M BisTris propane pH6.5, 0.2M Sodium Fluoride,20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.02 α = 90
b = 69.93 β = 90
c = 85.35 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 MARMOSAIC 225 mm CCD -- 2012-01-18
Diffraction Radiation
Monochromator Protocol
Si 111 double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.978 BESSY 14.2

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
1.45 50 95.9 0.033 -- -- 6.9 56080 53781 0.0 0.0 17.6
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)
1.45 1.5 74.2 0.258 -- 3.2 4.8 --

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 1.45 29.02 -- 0.0 53223 50998 2721 95.82 0.15108 0.15108 0.15 0.17109 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 1.45 1.486 -- 160 2698 0.179 0.225 -- 70.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.683
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.66
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_scbond_it 1.745
r_gen_planes_refined 0.008
r_dihedral_angle_2_deg 33.438
r_symmetry_vdw_refined 0.15
r_chiral_restr 0.096
r_nbd_refined 0.209
r_scangle_it 2.677
r_dihedral_angle_1_deg 5.484
r_nbtor_refined 0.321
r_mcangle_it 1.09
r_dihedral_angle_3_deg 11.636
r_dihedral_angle_4_deg 19.896
r_xyhbond_nbd_refined 0.152
r_symmetry_hbond_refined 0.221
r_angle_refined_deg 1.467
r_mcbond_it 0.754
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2342
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 500

Software

Software
Software Name Purpose
MarDB data collection
MOLREP phasing
REFMAC refinement version: 5.3.0037
HKL-3000 data reduction
HKL-3000 data scaling