X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details 0.2 M Potassium thiocyanate, 20 % w/v Polyethylene glycol 3,350, 10 mM Cadmium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.94 α = 90
b = 108.94 β = 90
c = 237.88 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-06-09
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97935 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 95.7 -- 0.103 -- 5.6 28517 28517 0.0 0.0 44.27
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 88.4 -- 0.741 1.8 4.1 1292

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 49.526 -- 0.0 26525 26525 1999 89.21 0.178 0.178 0.175 0.212 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 2.5001 2.5626 1522 115 1407 0.2784 0.3459 -- 73.0
X Ray Diffraction 2.5626 2.6319 1654 124 1530 0.2614 0.2904 -- 80.0
X Ray Diffraction 2.6319 2.7093 1729 131 1598 0.2436 0.3004 -- 83.0
X Ray Diffraction 2.7093 2.7968 1798 135 1663 0.2287 0.2574 -- 87.0
X Ray Diffraction 2.7968 2.8967 1840 139 1701 0.2152 0.2834 -- 89.0
X Ray Diffraction 2.8967 3.0127 1885 142 1743 0.2014 0.2749 -- 90.0
X Ray Diffraction 3.0127 3.1498 1919 145 1774 0.2132 0.2463 -- 92.0
X Ray Diffraction 3.1498 3.3158 1977 150 1827 0.1933 0.243 -- 94.0
X Ray Diffraction 3.3158 3.5235 1975 147 1828 0.1807 0.223 -- 94.0
X Ray Diffraction 3.5235 3.7955 2000 151 1849 0.1749 0.2142 -- 94.0
X Ray Diffraction 3.7955 4.1773 2013 151 1862 0.1579 0.1928 -- 94.0
X Ray Diffraction 4.1773 4.7813 2022 153 1869 0.1253 0.1522 -- 94.0
X Ray Diffraction 4.7813 6.0222 2061 155 1906 0.1432 0.1889 -- 94.0
X Ray Diffraction 6.0222 49.5354 2130 161 1969 0.161 0.1768 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 68.4
Anisotropic B[1][1] 8.0501
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.0501
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.1003
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.11
f_dihedral_angle_d 15.205
f_angle_d 1.273
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3465
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 116

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
phenix, phaser Structure Solution
PHENIX (phenix.refine: dev_761) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_761) refinement
phaser model building
phenix model building
HKL3000 data collection
SBCCOLLECT data collection