X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 295.0
Details Crystallization condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris pH 5.6. Freezing condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris 7% Glyserol,7% EG, 7% Sucrose. Protein: 3.4 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 27.47 α = 81.33
b = 34.71 β = 79.45
c = 61.93 γ = 70.07
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Mirror 2012-08-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.03316 APS 21-ID-D

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
1.4 30 95.6 0.068 -- -- 5.0 39510 39510 -- -3.0 14.4
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)
1.4 1.42 92.4 0.34 -- 3.8 3.5 1892

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
SAD 1.4 29.84 -- -- 33587 33587 1745 85.32 -- 0.14932 0.14737 0.18693 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 1.4 1.437 1345 79 1345 0.153 0.218 -- 45.98
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 14.227
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] -0.24
Anisotropic B[1][3] -0.04
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.02
Anisotropic B[3][3] -0.39
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.956
r_scbond_it 2.588
r_mcangle_it 1.959
r_mcbond_other 0.38
r_bond_refined_d 0.014
r_bond_other_d 0.001
r_angle_refined_deg 1.772
r_angle_other_deg 0.88
r_dihedral_angle_1_deg 2.748
r_dihedral_angle_2_deg 32.776
r_dihedral_angle_3_deg 8.198
r_dihedral_angle_4_deg 13.246
r_chiral_restr 0.119
r_gen_planes_refined 0.008
r_gen_planes_other 0.002
r_mcbond_it 1.194
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1896
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 302

Software

Computing
Computing Package Purpose
Blue Max Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000 Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
HKL3000 model building
Blue version: Max data collection