X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Mode
Temperature 277.0
Details 1 mL 40 mg/mL hemoglobin + 2.65 M (final concentration) phosphate buffer, topped with 100 uL toluene

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.73 α = 90
b = 53.73 β = 90
c = 192.29 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2016-04-14
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

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
2.28 51.75 95.88 -- -- -- 27.4 -- 13363 -- -- --
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)
2.28 -- -- -- -- -- -- --

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 2.28 51.748 -- 1.53 -- 13116 1312 95.88 -- 0.2088 0.205 0.2423 --
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 2.2801 2.3714 -- 133 1190 0.2192 0.2715 0.0 90.0
X Ray Diffraction 2.3714 2.4793 -- 136 1234 0.2145 0.2593 0.0 93.0
X Ray Diffraction 2.4793 2.61 -- 140 1252 0.2131 0.262 0.0 93.0
X Ray Diffraction 2.61 2.7735 -- 140 1268 0.2258 0.2599 0.0 96.0
X Ray Diffraction 2.7735 2.9877 -- 147 1315 0.2337 0.277 0.0 96.0
X Ray Diffraction 2.9877 3.2883 -- 144 1304 0.2252 0.2728 0.0 97.0
X Ray Diffraction 3.2883 3.764 -- 151 1355 0.1922 0.217 0.0 99.0
X Ray Diffraction 3.764 4.7417 -- 154 1388 0.1663 0.2165 0.0 99.0
X Ray Diffraction 4.7417 51.7611 -- 167 1498 0.2122 0.2303 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.9191
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.663
f_chiral_restr 0.034
f_bond_d 0.018
f_plane_restr 0.003
f_dihedral_angle_d 14.958
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2160
Nucleic Acid Atoms 0
Heterogen Atoms 150
Solvent Atoms 109

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: 1.12_2829
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHENIX phasing