X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3
Temperature 293.0
Details PEG 8000, sodium citrate, pH 3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.36 α = 90
b = 51.36 β = 90
c = 205.94 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9330 ESRF ID14-3
SYNCHROTRON ESRF BEAMLINE BM14 0.9791, 0.9794, 0.8856 ESRF BM14

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
1.95 30 95.6 -- -- -- -- 12606 12049 2.0 2.0 --
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)
1.95 2.001 95.6 -- -- -- -- --

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
MAD 1.95 30.0 -- 0.0 12606 12049 1239 95.58 -- 0.19232 0.18672 0.23844 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 1.95 2.001 -- 62 730 0.199 0.238 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.926
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.17
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 9.609
r_scbond_it 5.829
r_mcangle_it 3.344
r_mcbond_it 2.043
r_symmetry_hbond_refined 0.22
r_symmetry_vdw_refined 0.237
r_xyhbond_nbd_refined 0.225
r_bond_refined_d 0.04
r_angle_refined_deg 2.438
r_dihedral_angle_1_deg 3.741
r_dihedral_angle_3_deg 12.891
r_chiral_restr 0.225
r_gen_planes_refined 0.015
r_nbd_refined 0.234
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1029
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 189

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection