X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 105.0
Details PEG 8000, sodium cirate, ethylene glycol, sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 105K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.61 α = 74.08
b = 60.33 β = 63.3
c = 62.64 γ = 66.18
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic confocal mirrors 2001-09-20
Diffraction Radiation
Monochromator Protocol
Osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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 20 95.0 0.05 0.05 -- 3.9 43171 43171 0.0 -3.0 --
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)
2.0 2.07 91.5 0.179 0.179 6.1 3.7 4151

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 2.0 16.22 0.0 0.0 43166 43166 2161 95.0 0.208 0.20726 0.20441 0.2609 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 2.0 2.051 2851 145 2851 0.222 0.283 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 15.565
Anisotropic B[1][1] -0.64
Anisotropic B[1][2] -0.89
Anisotropic B[1][3] 0.28
Anisotropic B[2][2] 2.07
Anisotropic B[2][3] 0.35
Anisotropic B[3][3] -1.16
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.185
r_xyhbond_nbd_refined 0.123
r_symmetry_hbond_refined 0.121
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 3.649
r_angle_refined_deg 1.271
r_symmetry_vdw_refined 0.133
r_scbond_it 4.051
r_chiral_restr 0.083
r_mcangle_it 3.044
r_bond_refined_d 0.007
r_dihedral_angle_3_deg 19.343
r_mcbond_it 1.854
r_scangle_it 5.69
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5597
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 400

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
REFMAC refinement version: 5.0