X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 277.0
Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.19 α = 90
b = 103.68 β = 90
c = 138.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 85
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER SMART 6000 mirrors 2010-08-18
Diffraction Radiation
Monochromator Protocol
Osmic Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.54 -- --

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
2.25 57.7 98.6 0.0869 0.0869 -- 4.91 42133 41556 -3.0 -3.0 25.2
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)
2.25 2.34 87.5 0.3248 0.3248 2.53 2.35 4018

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 2.25 57.703 -- 1.34 -- 41479 2013 98.61 -- 0.1761 0.1743 0.2133 --
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 2.25 2.3063 -- 143 2325 0.2012 0.2358 -- 84.0
X Ray Diffraction 2.3063 2.3686 -- 137 2736 0.2067 0.2649 -- 97.0
X Ray Diffraction 2.3686 2.4384 -- 159 2805 0.1968 0.2655 -- 100.0
X Ray Diffraction 2.4384 2.5171 -- 139 2839 0.1946 0.2393 -- 100.0
X Ray Diffraction 2.5171 2.607 -- 148 2817 0.192 0.2485 -- 100.0
X Ray Diffraction 2.607 2.7114 -- 149 2811 0.1789 0.1965 -- 100.0
X Ray Diffraction 2.7114 2.8348 -- 144 2822 0.1688 0.2422 -- 100.0
X Ray Diffraction 2.8348 2.9842 -- 128 2860 0.1784 0.1887 -- 100.0
X Ray Diffraction 2.9842 3.1712 -- 166 2838 0.1745 0.2214 -- 100.0
X Ray Diffraction 3.1712 3.416 -- 138 2841 0.1702 0.2002 -- 100.0
X Ray Diffraction 3.416 3.7597 -- 139 2899 0.1672 0.233 -- 100.0
X Ray Diffraction 3.7597 4.3036 -- 146 2889 0.1479 0.1646 -- 100.0
X Ray Diffraction 4.3036 5.4215 -- 143 2925 0.1464 0.1798 -- 100.0
X Ray Diffraction 5.4215 57.722 -- 134 3059 0.1968 0.218 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.5539
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5501
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.0037
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.07
f_dihedral_angle_d 13.769
f_angle_d 1.045
f_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6202
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 697

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
PROTEUM PLUS Data Reduction (intensity integration)
PROTEUM PLUS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHASER model building
PROTEUM version: PLUS data collection