X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.8 α = 90
b = 128.8 β = 90
c = 72.91 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-08-31
Diffraction Radiation
Monochromator Protocol
double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-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
2.5 50 98.3 0.05 0.036 -- 7.9 21812 21439 2.0 2.0 --
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)
2.5 2.54 98.2 0.711 0.661 2.24 6.6 1046

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 2.5 45.199 -- 1.34 21792 21408 1997 98.24 -- 0.2072 0.2039 0.2398 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 2.5 2.5625 -- 137 1353 0.3011 0.3575 -- 97.0
X Ray Diffraction 2.5625 2.6318 -- 140 1356 0.2791 0.3531 -- 99.0
X Ray Diffraction 2.6318 2.7092 -- 140 1365 0.2367 0.301 -- 99.0
X Ray Diffraction 2.7092 2.7966 -- 145 1393 0.2358 0.2754 -- 100.0
X Ray Diffraction 2.7966 2.8966 -- 140 1364 0.249 0.3107 -- 99.0
X Ray Diffraction 2.8966 3.0125 -- 143 1380 0.2219 0.3129 -- 99.0
X Ray Diffraction 3.0125 3.1496 -- 142 1378 0.2175 0.2661 -- 99.0
X Ray Diffraction 3.1496 3.3156 -- 141 1379 0.2016 0.2346 -- 98.0
X Ray Diffraction 3.3156 3.5232 -- 142 1381 0.1982 0.2439 -- 99.0
X Ray Diffraction 3.5232 3.7951 -- 145 1404 0.1976 0.2382 -- 99.0
X Ray Diffraction 3.7951 4.1768 -- 142 1370 0.189 0.2511 -- 98.0
X Ray Diffraction 4.1768 4.7806 -- 143 1404 0.17 0.2041 -- 98.0
X Ray Diffraction 4.7806 6.0209 -- 145 1401 0.2065 0.2141 -- 97.0
X Ray Diffraction 6.0209 45.2064 -- 152 1483 0.2044 0.2165 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.2781
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.2781
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.5563
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 12.657
f_angle_d 1.096
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2437
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 21

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.refine: 1.7.1_743) model building
HKL-2000 data collection