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 = 30.72 α = 90
b = 69.28 β = 90
c = 64.53 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
IMAGE PLATE MARRESEARCH OSMICS --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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 2.54 20.0 -- -- -- 1952 198 88.2 -- 0.218 0.213 0.265 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 2.54 2.68 -- 14 143 0.311 0.373 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.68
Anisotropic B[1][1] -3.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.84
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 10.673
r_mcbond_it 1.302
r_symmetry_hbond_refined 0.311
r_nbd_refined 0.31
r_symmetry_vdw_refined 0.255
r_angle_other_deg 1.419
r_mcangle_it 2.208
r_scbond_it 3.722
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.172
r_scangle_it 5.564
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 447
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 15

Software

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