X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 295.0
Details 3.5-6% PEG 8000, 0.1M MES pH 6.1-6.3, 0.3M LiCl, 10mM MgCl2, vapor diffusion, hanging drop, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 207.21 α = 90
b = 207.21 β = 90
c = 203.22 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-01-30
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A

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
3.5 50 100.0 0.149 -- -- 9.9 63554 63554 1.0 1.0 --
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)
3.5 3.56 99.9 -- -- -- 5.5 --

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 3.5054 49.77 -- 1.33 63554 63330 3184 99.68 -- 0.2661 0.2631 0.3217 --
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 3.5054 3.5577 -- 143 2543 0.4001 0.4074 -- 98.0
X Ray Diffraction 3.5577 3.6133 -- 134 2584 0.3889 0.3838 -- 99.0
X Ray Diffraction 3.6133 3.6725 -- 154 2569 0.3844 0.3904 -- 100.0
X Ray Diffraction 3.6725 3.7358 -- 122 2579 0.3691 0.3949 -- 100.0
X Ray Diffraction 3.7358 3.8037 -- 150 2567 0.378 0.4219 -- 100.0
X Ray Diffraction 3.8037 3.8769 -- 151 2593 0.3408 0.3776 -- 100.0
X Ray Diffraction 3.8769 3.956 -- 137 2584 0.322 0.3786 -- 100.0
X Ray Diffraction 3.956 4.0419 -- 157 2592 0.3066 0.3725 -- 100.0
X Ray Diffraction 4.0419 4.1359 -- 108 2626 0.2831 0.3257 -- 100.0
X Ray Diffraction 4.1359 4.2393 -- 105 2636 0.2886 0.3588 -- 100.0
X Ray Diffraction 4.2393 4.3539 -- 134 2577 0.2692 0.3634 -- 100.0
X Ray Diffraction 4.3539 4.4819 -- 134 2618 0.2524 0.3501 -- 100.0
X Ray Diffraction 4.4819 4.6265 -- 119 2616 0.2316 0.3007 -- 100.0
X Ray Diffraction 4.6265 4.7917 -- 127 2612 0.2355 0.2606 -- 100.0
X Ray Diffraction 4.7917 4.9834 -- 140 2623 0.2393 0.2906 -- 100.0
X Ray Diffraction 4.9834 5.2099 -- 151 2601 0.2535 0.2991 -- 100.0
X Ray Diffraction 5.2099 5.4843 -- 161 2611 0.264 0.3188 -- 100.0
X Ray Diffraction 5.4843 5.8274 -- 130 2639 0.2611 0.3498 -- 100.0
X Ray Diffraction 5.8274 6.2766 -- 131 2639 0.2596 0.3402 -- 100.0
X Ray Diffraction 6.2766 6.9067 -- 175 2616 0.2527 0.3286 -- 100.0
X Ray Diffraction 6.9067 7.9027 -- 139 2645 0.2282 0.2974 -- 100.0
X Ray Diffraction 7.9027 9.9435 -- 138 2695 0.2063 0.2533 -- 100.0
X Ray Diffraction 9.9435 49.7752 -- 144 2781 0.2274 0.2913 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 117.367
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.061
f_dihedral_angle_d 15.901
f_angle_d 0.95
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23534
Nucleic Acid Atoms 863
Heterogen Atoms 3
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
CNS molecular replacement
SCALEPACK data reduction