X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 50 mM MES, pH 5.6, 300 mM potassium chloride, 10 mM magnesium chloride, 5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.7 α = 90
b = 110.7 β = 90
c = 58.78 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2012-04-17
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double crystal sagittal focusing Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.1 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
2.3 50 99.9 0.068 -- -- 5.7 35736 35736 0.0 0.0 52.34
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)
2.3 2.34 100.0 0.726 -- 2.3 5.6 1844

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 2.301 40.295 -- 1.96 35736 35711 1798 99.84 -- 0.1931 0.1904 0.246 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 2.301 2.3632 -- 140 2656 0.2551 0.3437 -- 100.0
X Ray Diffraction 2.3632 2.4328 -- 137 2560 0.2427 0.2868 -- 100.0
X Ray Diffraction 2.4328 2.5113 -- 129 2653 0.2408 0.3024 -- 100.0
X Ray Diffraction 2.5113 2.601 -- 141 2586 0.2317 0.3137 -- 100.0
X Ray Diffraction 2.601 2.7051 -- 146 2608 0.2375 0.3124 -- 100.0
X Ray Diffraction 2.7051 2.8282 -- 155 2631 0.2283 0.2549 -- 100.0
X Ray Diffraction 2.8282 2.9773 -- 137 2602 0.2157 0.2956 -- 100.0
X Ray Diffraction 2.9773 3.1637 -- 151 2582 0.2142 0.2886 -- 100.0
X Ray Diffraction 3.1637 3.4079 -- 152 2598 0.1994 0.2489 -- 100.0
X Ray Diffraction 3.4079 3.7506 -- 125 2629 0.1781 0.2624 -- 100.0
X Ray Diffraction 3.7506 4.2928 -- 138 2588 0.1658 0.2107 -- 100.0
X Ray Diffraction 4.2928 5.4064 -- 124 2640 0.1527 0.2061 -- 100.0
X Ray Diffraction 5.4064 40.3013 -- 123 2580 0.191 0.2203 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.3
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.07
f_dihedral_angle_d 16.112
f_angle_d 1.07
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4703
Nucleic Acid Atoms 160
Heterogen Atoms 0
Solvent Atoms 199

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX-AutoMR Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX-AutoMR model building
CBASS data collection