X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.2
Details 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.69 α = 90
b = 79.05 β = 117.88
c = 39.62 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2008-12-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- DIAMOND I04

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
1.5 39.53 99.2 0.04 -- -- 3.7 -- 32695 -- 2.0 23.082
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)
1.5 1.59 98.8 0.38 -- 3.4 3.65 --

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 1.5 33.064 -- 2.01 -- 32683 1686 99.57 -- 0.1911 0.1891 0.2276 --
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 1.5002 1.5444 -- 144 2531 0.2519 0.2776 -- 98.0
X Ray Diffraction 1.5444 1.5942 -- 155 2579 0.2317 0.294 -- 100.0
X Ray Diffraction 1.5942 1.6512 -- 144 2576 0.2351 0.2569 -- 100.0
X Ray Diffraction 1.6512 1.7173 -- 129 2601 0.2187 0.2805 -- 100.0
X Ray Diffraction 1.7173 1.7955 -- 141 2588 0.208 0.2709 -- 100.0
X Ray Diffraction 1.7955 1.8901 -- 145 2575 0.2006 0.2403 -- 100.0
X Ray Diffraction 1.8901 2.0085 -- 131 2591 0.1893 0.2327 -- 100.0
X Ray Diffraction 2.0085 2.1636 -- 155 2535 0.1869 0.2188 -- 100.0
X Ray Diffraction 2.1636 2.3813 -- 133 2619 0.1806 0.2198 -- 100.0
X Ray Diffraction 2.3813 2.7257 -- 135 2587 0.1849 0.1927 -- 100.0
X Ray Diffraction 2.7257 3.4335 -- 134 2603 0.1783 0.2262 -- 100.0
X Ray Diffraction 3.4335 33.0724 -- 140 2612 0.1653 0.1988 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.6366
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.7944
Anisotropic B[2][2] 0.0232
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6599
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.148
f_dihedral_angle_d 17.805
f_angle_d 1.577
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1714
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 305

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
AMORE Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
AMORE model building