X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 10% isopropanol, 200mM Lithium sulfate, citrate-phosphate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 166.24 α = 90
b = 166.24 β = 90
c = 166.24 γ = 90
Symmetry
Space Group I 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2002-11-10
Diffraction Radiation
Monochromator Protocol
Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-BM -- APS 17-BM

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
2.45 27.7 97.5 0.055 0.046 -- 4.2 14386 14386 0.0 0.0 39.0
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)
2.45 2.55 99.9 0.43 0.45 1.99 4.6 1610

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
MOLECULAR REPLACEMENT 2.45 27.7 0.0 0.0 14339 14339 721 97.39 0.218 0.21694 0.21454 0.26341 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 2.45 2.54 -- 59 1000 0.301 0.4 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 51.773
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.255
r_mcangle_it 4.563
r_scbond_it 7.532
r_symmetry_vdw_refined 0.249
r_xyhbond_nbd_refined 0.184
r_bond_refined_d 0.011
r_gen_planes_refined 0.008
r_symmetry_hbond_refined 0.219
r_chiral_restr 0.172
r_scangle_it 11.588
r_mcbond_it 2.666
r_angle_refined_deg 1.984
r_dihedral_angle_1_deg 8.692
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Resolution Cutoff (Low) 20.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1309
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 103

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing