X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 1.04M sodium malonate,100mM PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.7 α = 90
b = 77.7 β = 90
c = 395.47 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 1.033 APS 21-ID-G

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
2.2 50 97.1 0.115 -- -- 9.2 66210 66038 -- -- 31.5
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)
2.2 2.24 96.2 0.332 -- 4.9 6.6 3285

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 2.201 38.85 -- 1.36 -- 66038 2005 97.11 -- 0.1784 0.1776 0.2027 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 2.2009 2.2559 -- 143 4547 0.2178 0.2745 -- 97.0
X Ray Diffraction 2.2559 2.3169 -- 148 4713 0.2007 0.2602 -- 100.0
X Ray Diffraction 2.3169 2.385 -- 150 4671 0.1873 0.2281 -- 100.0
X Ray Diffraction 2.385 2.462 -- 152 4697 0.187 0.2526 -- 100.0
X Ray Diffraction 2.462 2.55 -- 143 4724 0.1907 0.2354 -- 100.0
X Ray Diffraction 2.55 2.6521 -- 143 4693 0.1909 0.2011 -- 100.0
X Ray Diffraction 2.6521 2.7727 -- 146 4739 0.1989 0.262 -- 100.0
X Ray Diffraction 2.7727 2.9189 -- 147 4667 0.2022 0.2704 -- 100.0
X Ray Diffraction 2.9189 3.1017 -- 148 4725 0.1879 0.2259 -- 100.0
X Ray Diffraction 3.1017 3.341 -- 143 4615 0.1726 0.1924 -- 99.0
X Ray Diffraction 3.341 3.677 -- 141 4421 0.1591 0.1685 -- 94.0
X Ray Diffraction 3.677 4.2086 -- 125 4109 0.1503 0.1696 -- 87.0
X Ray Diffraction 4.2086 5.3002 -- 132 4160 0.1555 0.1674 -- 88.0
X Ray Diffraction 5.3002 38.8565 -- 144 4554 0.1863 0.1784 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.7477
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.7477
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.7296
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.08
f_dihedral_angle_d 13.59
f_angle_d 1.277
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6819
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 426

Software

Computing
Computing Package Purpose
MC-2 diffractometer software from EMBL Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phnix.autoMR Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
Phnix.autoMR model building
MC-2 version: diffractometer software from EMBL data collection