X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 7 mg/mL frog M ferritin solution at pH 7.5 with TrisHCl. Precipitant: 2.1M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 210.74 α = 90
b = 210.74 β = 90
c = 322.04 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2010-12-10
Diffraction Radiation
Monochromator Protocol
channel cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 1.740 ESRF ID29

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
2.89 50.01 99.8 -- 0.129 -- 5.6 184115 184115 0.0 0.0 43.26
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)
2.89 3.05 100.0 0.182 -- 3.8 5.6 26736

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 2.89 48.537 -- 1.33 -- 184062 9239 99.72 -- 0.1751 0.1722 0.2286 --
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 2.89 2.9933 -- 920 17319 0.2187 0.2915 -- 100.0
X Ray Diffraction 2.9933 3.1131 -- 950 17329 0.2095 0.2984 -- 100.0
X Ray Diffraction 3.1131 3.2548 -- 883 17370 0.2066 0.2744 -- 100.0
X Ray Diffraction 3.2548 3.4263 -- 926 17408 0.1894 0.2608 -- 100.0
X Ray Diffraction 3.4263 3.6409 -- 934 17429 0.179 0.2399 -- 100.0
X Ray Diffraction 3.6409 3.9219 -- 936 17463 0.1635 0.2189 -- 100.0
X Ray Diffraction 3.9219 4.3164 -- 908 17523 0.1504 0.2005 -- 100.0
X Ray Diffraction 4.3164 4.9404 -- 877 17503 0.1473 0.1961 -- 99.0
X Ray Diffraction 4.9404 6.2224 -- 933 17642 0.1619 0.2141 -- 100.0
X Ray Diffraction 6.2224 48.5441 -- 972 17837 0.1604 0.1929 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0921
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0921
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1841
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_chiral_restr 0.075
f_dihedral_angle_d 17.648
f_plane_restr 0.004
f_angle_d 1.097
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 33960
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 919

Software

Computing
Computing Package Purpose
rotation 0.1 slices Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
rotation version: 0.1 slices data collection
MOLREP model building
PHENIX version: (phenix.refine: 1.6.4_486) refinement