X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Mode
Temperature 277.15
Details 1 mL of 40 mg/mL hemoglobin + 2.65 M (final concentration) phosphate buffer, topped with 100 uL toluene

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.43 α = 90
b = 83.12 β = 90
c = 83.68 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2015-12-14
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 1.00 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
1.32 37.72 99.7 0.105 -- -- 14.151 -- 72681 -- -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)
1.32 1.35 99.4 2.07 -- 1.42 13.345 --

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 1.58 37.715 -- 1.53 -- 69026 1997 94.94 -- 0.1831 0.1824 0.2071 --
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 1.58 1.6 -- 130 4262 0.2003 0.2362 0.0 85.0
X Ray Diffraction 1.6 1.621 -- 119 4203 0.1991 0.2178 0.0 85.0
X Ray Diffraction 1.621 1.6432 -- 136 4356 0.1977 0.2258 0.0 86.0
X Ray Diffraction 1.6432 1.6667 -- 131 4452 0.2011 0.2337 0.0 88.0
X Ray Diffraction 1.6667 1.6916 -- 124 4432 0.2073 0.2751 0.0 89.0
X Ray Diffraction 1.6916 1.718 -- 143 4453 0.206 0.2273 0.0 89.0
X Ray Diffraction 1.718 1.7462 -- 134 4544 0.2046 0.2144 0.0 91.0
X Ray Diffraction 1.7462 1.7763 -- 128 4599 0.2034 0.2518 0.0 91.0
X Ray Diffraction 1.7763 1.8086 -- 145 4632 0.1996 0.2389 0.0 92.0
X Ray Diffraction 1.8086 1.8434 -- 132 4640 0.2006 0.2128 0.0 93.0
X Ray Diffraction 1.8434 1.881 -- 144 4634 0.2011 0.1867 0.0 94.0
X Ray Diffraction 1.881 1.9219 -- 137 4779 0.1998 0.2447 0.0 95.0
X Ray Diffraction 1.9219 1.9666 -- 144 4853 0.1962 0.2083 0.0 96.0
X Ray Diffraction 1.9666 2.0158 -- 143 4837 0.1986 0.231 0.0 97.0
X Ray Diffraction 2.0158 2.0703 -- 137 4949 0.1946 0.2584 0.0 98.0
X Ray Diffraction 2.0703 2.1312 -- 144 4961 0.1798 0.2064 0.0 99.0
X Ray Diffraction 2.1312 2.2 -- 149 4967 0.1787 0.1856 0.0 99.0
X Ray Diffraction 2.2 2.2786 -- 153 4906 0.1869 0.2069 0.0 98.0
X Ray Diffraction 2.2786 2.3698 -- 142 4976 0.1782 0.1983 0.0 99.0
X Ray Diffraction 2.3698 2.4777 -- 150 4953 0.1842 0.2034 0.0 99.0
X Ray Diffraction 2.4777 2.6083 -- 159 5009 0.1939 0.2283 0.0 100.0
X Ray Diffraction 2.6083 2.7716 -- 149 4965 0.1863 0.2211 0.0 100.0
X Ray Diffraction 2.7716 2.9855 -- 150 5020 0.1852 0.2213 0.0 100.0
X Ray Diffraction 2.9855 3.2858 -- 146 5005 0.1809 0.2154 0.0 100.0
X Ray Diffraction 3.2858 3.7609 -- 154 5029 0.1631 0.1751 0.0 100.0
X Ray Diffraction 3.7609 4.7369 -- 144 4982 0.1435 0.1603 0.0 100.0
X Ray Diffraction 4.7369 37.7257 -- 161 5005 0.1881 0.2097 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.8582
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.484
f_angle_d 0.899
f_plane_restr 0.007
f_chiral_restr 0.051
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4304
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 702

Software

Software
Software Name Purpose
HKL-2000 data collection
XSCALE data scaling
PHENIX refinement version: 1.11.1_2575
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHENIX phasing