X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details 0.1M Tris-HCl, 0.2M NaCl, 20% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.47 α = 90
b = 107.93 β = 90
c = 117.12 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 -- 2010-09-21
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9789 SSRF BL17U

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
2.3 80 100.0 -- -- -- -- 19579 19579 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)
2.3 2.38 100.0 -- -- -- -- --

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 2.3 20.0 -- 0.0 18436 18436 994 98.73 0.18404 0.18403 0.1816 0.23029 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 2.3 2.36 -- 69 1249 0.193 0.274 -- 91.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.134
Anisotropic B[1][1] -0.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.41
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.086
r_scbond_it 3.628
r_mcangle_it 1.967
r_mcbond_it 1.013
r_gen_planes_refined 0.011
r_chiral_restr 0.074
r_dihedral_angle_4_deg 11.963
r_dihedral_angle_3_deg 16.191
r_dihedral_angle_2_deg 33.268
r_dihedral_angle_1_deg 7.697
r_angle_refined_deg 0.938
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2636
Nucleic Acid Atoms 697
Heterogen Atoms 4
Solvent Atoms 149

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHENIX model building
MAR345dtb data collection