X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 287.0
Details 0.1M Sodium acetate, 2M sodium formate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.88 α = 90
b = 74.45 β = 107.77
c = 108.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2011-10-08
Diffraction Radiation
Monochromator Protocol
Double MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 PHOTON FACTORY AR-NE3A

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
2.4 20 94.1 -- -- -- -- 37665 35640 0.0 0.0 --
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)
2.4 2.44 86.1 -- -- -- -- --

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 2.4 19.98 -- 1.54 37665 35640 1981 93.93 -- 0.201 0.1974 0.2633 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 2.4 2.4577 -- 127 2236 0.2671 0.3274 -- 84.0
X Ray Diffraction 2.4577 2.524 -- 133 2360 0.2437 0.349 -- 88.0
X Ray Diffraction 2.524 2.5982 -- 127 2369 0.234 0.2623 -- 87.0
X Ray Diffraction 2.5982 2.6818 -- 136 2422 0.2327 0.3149 -- 90.0
X Ray Diffraction 2.6818 2.7774 -- 134 2476 0.2369 0.3064 -- 92.0
X Ray Diffraction 2.7774 2.8883 -- 139 2571 0.2403 0.3441 -- 95.0
X Ray Diffraction 2.8883 3.0194 -- 149 2592 0.2223 0.2852 -- 96.0
X Ray Diffraction 3.0194 3.178 -- 150 2597 0.2065 0.2745 -- 97.0
X Ray Diffraction 3.178 3.3762 -- 141 2593 0.1931 0.2785 -- 96.0
X Ray Diffraction 3.3762 3.6354 -- 146 2615 0.1854 0.2459 -- 96.0
X Ray Diffraction 3.6354 3.9986 -- 148 2661 0.1744 0.2369 -- 98.0
X Ray Diffraction 3.9986 4.5712 -- 147 2695 0.1668 0.2116 -- 99.0
X Ray Diffraction 4.5712 5.7365 -- 148 2720 0.1791 0.1921 -- 99.0
X Ray Diffraction 5.7365 19.9803 -- 156 2753 0.22 0.2659 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.3982
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 10.6891
Anisotropic B[2][2] -11.9694
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.5713
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.091
f_dihedral_angle_d 18.052
f_angle_d 1.278
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7021
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 244

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CCP4 Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
CCP4 model building
HKL-2000 data collection