X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 291.0
Details PEG 3350, PEG 400, Tris, NaI, glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.03 α = 90
b = 48.27 β = 90
c = 183.04 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 ADSC QUANTUM 4 -- 2000-10-10
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.65 45 98.1 -- 0.068 -- 5.8 49451 49451 6.0 6.0 19.562
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)
1.65 1.69 90.7 -- 0.373 5.9 5.5 2966

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
experimental phases derived from SAD data (iodide ions) 1.65 44.72 -- 1.0 45286 45286 3942 99.54 -- 0.16867 0.1653 0.20857 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 1.65 1.708 -- 356 4188 0.172 0.241 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.834
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.21
r_nbd_refined 0.245
r_bond_refined_d 0.016
r_chiral_restr 0.119
r_mcbond_it 3.538
r_gen_planes_refined 0.007
r_angle_other_deg 1.481
r_symmetry_hbond_refined 0.351
r_angle_refined_deg 1.617
r_bond_other_d 0.002
r_dihedral_angle_2_deg 16.102
r_symmetry_vdw_refined 0.466
r_scbond_it 43.315
r_symmetry_vdw_other 0.424
r_mcangle_it 8.496
r_gen_planes_other 0.003
r_scangle_it 40.211
r_nbd_other 0.226
r_xyhbond_nbd_refined 0.325
r_dihedral_angle_1_deg 4.883
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2742
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 462

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
SOLOMON phasing
ARP/wARP model building