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 = 127.28 α = 90
b = 127.28 β = 90
c = 73.99 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 2011-10-20
Diffraction Radiation
Monochromator Protocol
double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97915 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
1.97 50 99.6 0.077 0.071 -- 9.8 43957 43789 2.0 2.0 40.5
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)
1.97 2.0 97.7 0.937 0.854 2.08 8.0 2098

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 1.97 40.249 -- 1.35 43743 41745 2000 99.5 -- 0.1984 0.1974 0.2202 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 1.9626 2.0116 -- 136 2834 0.2904 0.3222 -- 96.0
X Ray Diffraction 2.0116 2.066 -- 140 2920 0.2254 0.2445 -- 99.0
X Ray Diffraction 2.066 2.1268 -- 141 2943 0.2077 0.2494 -- 100.0
X Ray Diffraction 2.1268 2.1955 -- 142 2962 0.1889 0.2127 -- 100.0
X Ray Diffraction 2.1955 2.2739 -- 140 2929 0.1873 0.2014 -- 100.0
X Ray Diffraction 2.2739 2.365 -- 141 2956 0.1889 0.2588 -- 100.0
X Ray Diffraction 2.365 2.4726 -- 143 2980 0.1979 0.2198 -- 100.0
X Ray Diffraction 2.4726 2.6029 -- 142 2967 0.1988 0.197 -- 100.0
X Ray Diffraction 2.6029 2.766 -- 143 2977 0.1975 0.2114 -- 100.0
X Ray Diffraction 2.766 2.9795 -- 144 3000 0.2104 0.2335 -- 100.0
X Ray Diffraction 2.9795 3.2792 -- 144 3010 0.2016 0.2345 -- 100.0
X Ray Diffraction 3.2792 3.7534 -- 146 3033 0.1968 0.2016 -- 100.0
X Ray Diffraction 3.7534 4.7277 -- 145 3055 0.1745 0.1938 -- 100.0
X Ray Diffraction 4.7277 40.257 -- 153 3177 0.2062 0.2422 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.7609
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.7609
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.5218
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.066
f_dihedral_angle_d 19.489
f_angle_d 1.111
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2478
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 118

Software

Computing
Computing Package Purpose
HKL-3000 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-3000 data collection