X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 293.0
Details 0.1 M MgCl2, 20% PEG 3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.55 α = 90
b = 52.61 β = 109.22
c = 63.65 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 QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 1.0000 APS 24-ID-E

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
2.1 29.25 96.39 -- 0.073 -- 3.2 15780 n/a 2.0 0.0 46.37
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)
2.1 2.26 87.9 -- 0.329 -- 2.6 --

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 2.095 29.249 -- 1.37 15780 15211 755 96.4 -- 0.1817 0.1788 0.2408 --
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 2.0953 2.257 -- 150 2615 0.2246 0.2838 -- 88.0
X Ray Diffraction 2.257 2.484 -- 138 2832 0.2194 0.2992 -- 95.0
X Ray Diffraction 2.484 2.8432 -- 166 2964 0.2145 0.2982 -- 99.0
X Ray Diffraction 2.8432 3.5811 -- 155 2989 0.1995 0.293 -- 100.0
X Ray Diffraction 3.5811 29.2519 -- 146 3056 0.1517 0.1879 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.1
Anisotropic B[1][1] -3.5863
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.4565
Anisotropic B[2][2] -7.0564
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.6427
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 14.614
f_angle_d 1.064
f_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2051
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 87

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6_289) refinement
PHENIX version: (phenix.automr) model building
ADSC version: Quantum data collection