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 M 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 = 166.03 α = 90
b = 37.44 β = 125.5
c = 100.56 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
-- 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
2.2 50 99.5 0.103 -- -- 4.4 -- 25485 -- -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)
2.2 2.28 98.3 0.454 -- -- 2.9 2480

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 2.2 41.59 -- 0.0 27004 24563 2441 94.09 -- 0.2023 0.1972 0.2496 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 2.2 2.257 -- 116 1075 0.289 0.322 -- 63.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.4621
Anisotropic B[1][1] -1.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.32
Anisotropic B[2][2] -0.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.7
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.073
r_scbond_it 1.315
r_mcangle_it 0.705
r_mcbond_other 0.084
r_mcbond_it 0.641
r_symmetry_hbond_refined 0.199
r_symmetry_vdw_other 0.282
r_symmetry_vdw_refined 0.199
r_xyhbond_nbd_refined 0.174
r_nbtor_other 0.082
r_nbtor_refined 0.178
r_nbd_other 0.192
r_bond_refined_d 0.011
r_bond_other_d 0.009
r_angle_refined_deg 1.416
r_angle_other_deg 0.99
r_dihedral_angle_1_deg 5.799
r_dihedral_angle_2_deg 33.556
r_dihedral_angle_3_deg 15.733
r_dihedral_angle_4_deg 12.88
r_chiral_restr 0.076
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_nbd_refined 0.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2686
Nucleic Acid Atoms 186
Heterogen Atoms 98
Solvent Atoms 167

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