X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 166.41 α = 90
b = 37.73 β = 125.43
c = 101.63 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Rh coated Si vertical focus mirror 2007-01-01
Diffraction Radiation
Monochromator Protocol
Horizontal focusing 5.05? asymmetric cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.987 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
2.16 50 98.9 0.14 -- -- 5.7 -- 27427 -- -1.0 --
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)
2.16 2.24 92.1 0.365 -- -- 4.2 --

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
FOURIER SYNTHESIS 2.17 41.42 -- -- 29877 24457 2710 97.69 -- 0.1924 0.18837 0.22944 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 2.17 2.226 -- 166 1506 0.203 0.269 -- 82.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.7193
Anisotropic B[1][1] -0.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.01
Anisotropic B[2][2] -1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.917
r_scbond_it 1.152
r_mcangle_it 0.653
r_mcbond_it 0.571
r_nbd_refined 0.176
r_gen_planes_other 0.001
r_gen_planes_refined 0.003
r_dihedral_angle_4_deg 16.451
r_dihedral_angle_3_deg 13.951
r_dihedral_angle_2_deg 34.638
r_dihedral_angle_1_deg 5.249
r_angle_other_deg 1.187
r_angle_refined_deg 1.257
r_bond_other_d 0.001
r_bond_refined_d 0.008
r_nbd_other 0.179
r_nbtor_refined 0.174
r_nbtor_other 0.08
r_xyhbond_nbd_refined 0.133
r_symmetry_vdw_refined 0.123
r_symmetry_vdw_other 0.152
r_symmetry_hbond_refined 0.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2686
Nucleic Acid Atoms 262
Heterogen Atoms 116
Solvent Atoms 272

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement
SCALEPACK data reduction
DENZO data collection