X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 289.0
Details 30% polyethylene glycol (PEG) 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.96 α = 90
b = 53.72 β = 96.49
c = 81.56 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror 2011-10-24
Diffraction Radiation
Monochromator Protocol
-- 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
2.49 39.16 99.1 0.081 -- -- 10.2 -- 13702 -- -3.0 58.71
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)
2.49 2.58 93.6 0.63 -- 2.9 8.5 1282

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 2.493 39.161 -- 1.34 -- 13673 680 98.73 -- 0.2259 0.2239 0.2665 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 2.493 2.6854 -- 119 2476 0.384 0.4923 -- 95.0
X Ray Diffraction 2.6854 2.9556 -- 153 2583 0.3314 0.392 -- 100.0
X Ray Diffraction 2.9556 3.3831 -- 143 2596 0.2307 0.3172 -- 100.0
X Ray Diffraction 3.3831 4.2615 -- 123 2644 0.2169 0.2367 -- 100.0
X Ray Diffraction 4.2615 39.1656 -- 142 2694 0.1853 0.2158 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 25.2992
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 16.1207
Anisotropic B[2][2] -10.7805
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.5187
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.056
f_dihedral_angle_d 23.614
f_angle_d 0.863
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1525
Nucleic Acid Atoms 1139
Heterogen Atoms 10
Solvent Atoms 38

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
PHENIX model building
HKL-2000 data collection