X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.78 α = 90
b = 69.47 β = 90
c = 65 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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 98.3 0.037 -- -- 3.5 -- 4839 -- -- --
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 95.8 0.203 -- 12.0 -- --

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
MOLECULAR REPLACEMENT 2.0 20.0 -- -- -- 4620 219 98.0 -- 0.24 0.237 0.295 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 2.11 -- 37 645 0.272 0.305 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.5
Anisotropic B[1][1] -1.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.0
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 8.17
r_xyhbond_nbd_refined 0.312
r_scangle_it 4.392
r_symmetry_hbond_refined 0.358
r_mcangle_it 2.298
r_nbd_refined 0.28
r_angle_other_deg 1.588
r_symmetry_vdw_refined 0.205
r_scbond_it 3.532
r_bond_refined_d 0.014
r_mcbond_it 1.569
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 470
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 30

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing