X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Temperature 298.0
Details PEG 10000, Bis Tris HCl, CH3COOHNH4, pH 5.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.79 α = 90
b = 67.79 β = 90
c = 94.11 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-03-09
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 -- SSRL BL12-2

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
2.21 38.66 92.2 -- 0.161 -- 5.3 -- 20621 -- -3.0 --
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)
2.21 2.33 65.4 0.691 0.691 1.1 4.6 --

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 38.656 -- 1.35 17535 16831 834 95.99 -- 0.2031 0.201 0.249 --
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 2.4001 2.5505 -- 145 2686 0.2564 0.3508 -- 99.0
X Ray Diffraction 2.5505 2.7474 -- 141 2704 0.2497 0.335 -- 98.0
X Ray Diffraction 2.7474 3.0237 -- 140 2695 0.2317 0.281 -- 99.0
X Ray Diffraction 3.0237 3.461 -- 139 2634 0.209 0.2413 -- 96.0
X Ray Diffraction 3.461 4.3596 -- 131 2621 0.1707 0.2228 -- 93.0
X Ray Diffraction 4.3596 38.6611 -- 138 2657 0.176 0.1808 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.26
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.053
f_dihedral_angle_d 12.942
f_angle_d 0.949
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3271
Nucleic Acid Atoms 0
Heterogen Atoms 141
Solvent Atoms 146

Software

Computing
Computing Package Purpose
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction