X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 290.0
Details 0.1M imidazole, 1.0M sodium acetate, 10 mM YCl3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.92 α = 90
b = 78.92 β = 90
c = 197.92 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-05-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 3W1A 1.0 BSRF 3W1A

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
2.39 50 100.0 -- -- -- -- 11047 11047 2.0 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)
2.85 2.95 100.0 -- -- -- -- --

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
MIR 2.39 39.47 -- 2.0 8685 8425 967 96.92 0.22331 0.22331 0.2183 0.2664 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 2.393 2.454 -- 56 531 0.26 0.366 -- 84.58
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.261
Anisotropic B[1][1] 0.3
Anisotropic B[1][2] 0.15
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.45
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.955
r_scbond_it 3.474
r_mcangle_it 2.761
r_mcbond_it 1.826
r_symmetry_hbond_refined 0.332
r_bond_refined_d 0.029
r_angle_refined_deg 2.668
r_dihedral_angle_1_deg 10.453
r_dihedral_angle_2_deg 32.942
r_dihedral_angle_3_deg 26.393
r_dihedral_angle_4_deg 15.483
r_chiral_restr 0.224
r_gen_planes_refined 0.013
r_nbd_refined 0.302
r_nbtor_refined 0.343
r_xyhbond_nbd_refined 0.268
r_symmetry_vdw_refined 0.518
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1479
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 59

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
SOLVE model building
CrystalClear data collection