X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Diffusion
pH 6.8
Temperature 295.0
Details sodium phosphate, potassium phosphate, nitrite, toluene, hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.49 α = 90
b = 53.49 β = 90
c = 190 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
IMAGE PLATE RIGAKU RAXIS IV++ Osmic 2010-03-17
Diffraction Radiation
Monochromator Protocol
Osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.9 27.2 100.0 -- -- -- -- 22776 22697 2.0 2.0 --
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)
1.9 1.97 100.0 -- -- -- -- --

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 1.9 27.2 -- 1.34 22776 22697 1162 99.89 -- 0.21 0.2072 0.2625 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 1.9 1.9865 -- 157 2613 0.2258 0.2682 -- 100.0
X Ray Diffraction 1.9865 2.0912 -- 123 2624 0.2204 0.3117 -- 100.0
X Ray Diffraction 2.0912 2.2221 -- 159 2640 0.2184 0.3151 -- 100.0
X Ray Diffraction 2.2221 2.3936 -- 161 2624 0.2311 0.2864 -- 100.0
X Ray Diffraction 2.3936 2.6343 -- 123 2669 0.2244 0.293 -- 100.0
X Ray Diffraction 2.6343 3.0151 -- 148 2702 0.223 0.2735 -- 100.0
X Ray Diffraction 3.0151 3.797 -- 145 2748 0.1916 0.2426 -- 100.0
X Ray Diffraction 3.797 27.252 -- 146 2915 0.1826 0.213 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 32.79
Anisotropic B[1][1] 0.1438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1438
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2876
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 1.11
f_chiral_restr 0.064
f_bond_d 0.007
f_dihedral_angle_d 15.913
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2191
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 166

Software

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.6_289)
d*TREK data reduction
d*TREK data scaling